Description

BMC Genomics publishes original research articles in all aspects of gene mapping, sequencing and analysis, functional genomics, and proteomics.

Publications in this journal

• Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2.

  Authors: Christina B Garcia, Christian M Shaffer, Josiane E Eid

  BMC genomics. 13(1):189.

  ABSTRACT: BACKGROUND: SYT-SSX is the oncogene associated with synovial sarcoma (SS), a stem cell disease. SYT-SSX is thought to be responsible for sarcoma initiation and development. It interactsABSTRACT: BACKGROUND: SYT-SSX is the oncogene associated with synovial sarcoma (SS), a stem cell disease. SYT-SSX is thought to be responsible for sarcoma initiation and development. It interacts with components of Polycomb and SWI/SNF complexes, the two epigenetic controllers that maintain the heritable status of differentiation-specific genes in the stem/progenitor cell. Through these associations SYT-SSX is thought to alter gene expression programs by epigenetic mechanisms. Recently, we reported that SYT-SSX2 reprograms mesenchymal stem cells and myoblasts by dictating their commitment to the neural lineage while disrupting their normal differentiation. This reprogramming was due to the direct occupancy of proneural genes by the SYT-SSX2 nuclear complex. To gain a clear understanding of SYT-SSX2 control of gene expression networks, we conducted a thorough genome-wide analysis to determine the mechanism of its recruitment and identify signature sets of epigenetic markers that would predict its targeting and transcriptional activity. RESULTS: SYT-SSX2 was recruited to distinct loci across all chromosomes, and an overwhelming number of Polycomb-modified sites enriched with the trimethylated histone H3 on lysine 27 (H3K27me3) formed the main recruiting module for SYT-SSX2. Not all SYT-SSX2/ H3K27me3-occupied genes had altered expression, denoting the requirement for additional signals upon oncogene binding. Differential binding and epigenetic patterns distinguished upregulated and downregulated genes. Most activated genes had SYT-SSX2 sites enriched with H3K27me3 within their body or near their transcription start site (TSS) whereas a majority of downregulated genes were characterized by SYT-SSX2/H3K27me3-rich regions at long-range, or by modifications associated with transcription activation within the gene body or near the TSS. Hierarchical and functional clustering identified H3K27me3 as the dominant epigenetic marker associated with SYT-SSX2 binding and gene expression. Notably, this analysis revealed a cluster of upregulated neuronal genes densely covered by H3K27me3, consistent with programming toward the neural lineage by SYT-SSX2 observed previously. CONCLUSIONS: the data analysis revealed that Polycomb complexes or their modified chromatin and their stably silenced differentiation programs seem to be the main target for SYT-SSX2, suggesting that their perturbation is at the center of tumorigenesis driven by the oncogene. Further research into this mechanism is crucial to the full understanding of SS biology.

• Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks.

  Authors: Monika Ray, Reem Yunis, Xiucui Chen, David Rocke

  BMC genomics. 13(1):190.

  ABSTRACT: The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiationABSTRACT: The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documented, the detrimental effects of LDIR is not well understood and has been a topic of much debate. Since little is known about the effects of LDIR, various kinds of wet-lab and computational analyses are required to advance knowledge in this domain. In this paper we carry out an "upside-down pyramid" form of systems biology analysis of microarray data. We characterised the global genomic response following 10 cGy (low dose) and 100 cGy (high dose) doses of X-ray ionising radiation at four time points by analysing the topology of gene coexpression networks. This study includes a rich experimental design and state-of-the-art computational systems biology methods of analysis to study the differences in the transcriptional response of skin cells exposed to low and high doses of radiation. Using this method we found important genes that have been linked to immune response, cell survival and apoptosis. Furthermore, we also were able to identify genes such as BRCA1, ABCA1, TNFRSF1B, MLLT11 thats have been associated with various types of cancers. Our method of applying network topological differences can aid in identifying the differences among similar (eg: radiation effect) yet very different biological conditions (eg: different dose and time) to generate testable hypotheses. This is the first study where a network level analysis was performed across two different radiation doses at various time points, thereby illustrating changes in the cellular response over time.

• Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content.

  Authors: Jacob Abel, Jan Mrazek

  BMC genomics. 13(1):188.

  ABSTRACT: BACKGROUND: Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending isABSTRACT: BACKGROUND: Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in many prokaryotic genomes is not clear. RESULTS: We developed measures of intensity and persistency of DNA curvature-related sequence periodicity and applied them to prokaryotic chromosomes and phages. The results indicate that strong periodic signals present in chromosomes are generally absent in phage genomes. Moreover, chromosomes containing prophages are less likely to possess a persistent periodic signal than chromosomes with no prophages. CONCLUSIONS: Absence of DNA curvature-related sequence periodicity in phages could arise from constraints associated with DNA packaging in the viral capsid. Lack of prophages in chromosomes with persistent periodic signal suggests that the sequence periodicity and concomitant DNA curvature could play a role in protecting the chromosomes from integration of phage DNA.

• Transcription profiling reveals stage- and functiondependent expression patterns in the filarial nematode brugia malayi.

  Authors: Ben-Wen Li, Zhenyuan Wang, Amy C Rush, Makedonka Mitriva, Gary J Weil

  BMC genomics. 13(1):184.

  ABSTRACT: BACKGROUND: Brugia malayi is a nematode parasite that causes lymphatic filariasis, a disfiguring and disabiling tropical disease. Although a first draft genome sequence was released inABSTRACT: BACKGROUND: Brugia malayi is a nematode parasite that causes lymphatic filariasis, a disfiguring and disabiling tropical disease. Although a first draft genome sequence was released in 2007, very little is understood about transcription programs that govern developmental changes required for the parasite's development and survival in its mammalian and insect hosts. RESULTS: We used a microarray with probes that represent some 85% of predicted genes to generate gene expression profiles for seven parasite life cycle stages/sexes. Approximately 41% of transcripts with detectable expression signals were differentially expressed across lifecycle stages. Twenty-six percent of transcripts were exclusively expressed in a single parasite stage, and 27% were expressed in all stages studied. K-means clustering of differentially expressed transcripts revealed five major transcription patterns that were associated with parasite lifecycle stages or gender. Examination of known stage-associated transcripts validated these data sets and suggested that newly identified stage or gender-associated transcripts may exercise biological functions in development and reproduction. The results also indicate that genes with similar transcription patterns were often involved in similar functions or cellular processes. For example, nuclear receptor family gene transcripts were upregulated in gene expression pattern four (female-enriched) while protein kinase gene family transcripts were upregulated in expression pattern five (male-enriched). We also used pair-wise comparisons to identify transcriptional changes between life cycle stages and sexes. CONCLUSIONS: Analysis of gene expression patterns of lifecycle in B. malayi has provided novel insights into the biology of filarial parasites. Proteins encoded by stage-associated and/or stage-specific transcripts are likely to be critically important for key parasite functions such as establishment and maintenance of infection, development, reproduction, and survival in the host. Some of these may be useful targets for vaccines or new drug treatments for filariasis.

• Development and application of a 6.5 million feature affymetrix genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).

  Authors: Kevin Stoffel, Hans van Leeuwen, Alexander Kozik, David Caldwell, Hamid Ashrafi, Xinping Cui, Xiaoping Tan, Theresa Hill, Sebastian Reyes-Chin-Wo, Maria-Jose Truco, Richard W Michelmore, Allen Van Deynze

  BMC genomics. 13(1):185.

  ABSTRACT: BACKGROUND: High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays toABSTRACT: BACKGROUND: High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS: We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION: By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise.

• Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin c content in tomato fruit.

  Authors: Viviana Lima-Silva, Abel Rosado, Vitor Amorin-Silva, Antonio Muñoz-Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A Botella

  BMC genomics. 13(1):187.

  ABSTRACT: BACKGROUND: L-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as themain hydrosoluble antioxidant. It has diverse roles in the regulation of plant cellABSTRACT: BACKGROUND: L-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as themain hydrosoluble antioxidant. It has diverse roles in the regulation of plant cell growth andexpansion, photosynthesis, and hormone-regulated processes. AsA is also an essentialcomponent of the human diet, being tomato fruit one of the main sources of this vitamin. Toidentify genes responsible for AsA content in tomato fruit, transcriptomic studies followed byclustering analysis were applied to two groups of fruits with contrasting AsA content. Thesefruits were identified after AsA profiling of an F8 Recombinant Inbred Line (RIL) populationgenerated from a cross between the domesticated species Solanum lycopersicum and the wildrelative Solanum pimpinellifollium. RESULTS: We found large variability in AsA content within the RIL population with individual RILswith up to 4-fold difference in AsA content. Transcriptomic analysis identified genes whoseexpression correlated either positively (PVC genes) or negatively (NVC genes) with the AsAcontent of the fruits. Cluster analysis using SOTA allowed the identification of subsets of coregulatedgenes mainly involved in hormones signaling, such as ethylene, ABA, gibberellinand auxin, rather than any of the known AsA biosynthetic genes. Data mining of thecorresponding PVC and NVC orthologs in Arabidopis databases identified flagellin and otherROS-producing processes as cues resulting in differential regulation of a high percentage ofthe genes from both groups of co-regulated genes; more specifically, 26.6% of theorthologous PVC genes, and 15.5% of the orthologous NVC genes were induced andrepressed, respectively, under flagellin22 treatment in Arabidopsis thaliana. CONCLUSION: Results here reported indicate that the content of AsA in red tomato fruit from our selectedRILs are not correlated with the expression of genes involved in its biosynthesis. On the contrary, the data presented here supports that AsA content in tomato fruit co-regulates withgenes involved in hormone signaling and they are dependent on the oxidative status of thefruit.

• Identification of avian W-linked contigs by short-read sequencing.

  Authors: Nancy Chen, Daniel W Bellott, David C Page, Andrew G Clark

  BMC genomics. 13(1):183.

  ABSTRACT: BACKGROUND: The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches toABSTRACT: BACKGROUND: The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identifying sequences that are W-specific. RESULTS: Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 60 novel W-specific sequences. CONCLUSIONS: Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution.

• Estimating RNA-quality using GeneChip microarrays.

  Authors: Mario Fasold, Hans Binder

  BMC genomics. 13(1):186.

  ABSTRACT: BACKGROUND: Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrityABSTRACT: BACKGROUND: Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrity can lead to low data quality and failure of the microarray experiment. RESULTS: Microarray intensity data contains information to estimate the RNA quality of the sample. We here study the interplay of the characteristics of RNA surface hybridization with the effects of partly truncated transcripts on probe intensity. The 3'/5' intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distance of the probe from the 3'-end of the transcript. Increasing degrees of non-specific hybridization or of saturation reduce the 3'/5' intensity gradient and if not taken into account, this leads to biased results in common quality measures for GeneChip arrays such as affyslope or the control probe intensity ratio. We also found that short probe sets near the 3'-end of the transcripts are prone to non-specific hybridization presumable because of inaccurate positional assignment and the existence of transcript isoforms with variable 3' UTR's . Poor RNA quality is associated with a decreased amount of RNA material hybridized on the array paralleled by a decreased total signal level. Additionally, it causes a gene-specific loss of signal due to the positional bias of transcript abundance which requires an individual, gene-specific correction. We propose a new RNA quality measure that considers the hybridization mode. Graphical characteristics are introduced allowing assessment of RNA quality of each single array ('tongs plot' and 'degradation hook'). Furthermore, we suggest a method to correct for effects of RNA degradation on microarray intensities. CONCLUSIONS: The presented RNA degradation measure has best correlation with the independent RNA integrity measure RIN, and therefore presents itself as a valuable tool for quality control and even for the study of RNA degradation. When RNA degradation effects are detected in microarray experiments, a correction of the induced bias in probe intensities is advised.

• Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing.

  Authors: Daniel Garcia de la Serrana Castillo, Alicia Estevez, Karl Andree, Ian A Johnston

  BMC genomics. 13(1):181.

  ABSTRACT: BACKGROUND: The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range ofABSTRACT: BACKGROUND: The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is often found in brackish coastal lagoons and estuarine areas, particularly early in its life cycle. Gilthead sea bream are extensively cultivated in the Mediterranean with an annual production of 125,000 metric tonnes. Here we present a de novo assembly of the fast skeletal muscle transcriptome of gilthead sea bream using 454 reads and identify gene paralogues, splice variants and microsatellite repeats. An annotated transcriptome of the skeletal muscle will facilitate understanding of the genetic and molecular basis of traits linked to production in this economically important species. RESULTS: Around 2.7 million reads of mRNA sequence data were generated from the fast myotomal of adult fish (~2 kg) and juvenile fish (~0.09 kg) that had been either fed to satiation, fasted for 3-5d or transferred to low (11degreesC) or high (33degreesC) temperatures for 3-5d. Newbler v2.5 assembly resulted in 43,461 isotigs >100 bp. The number of sequences annotated by searching protein and gene ontology databases was 10,465. The average coverage of the annotated isotigs was x40 containing 5655 unique gene IDs and 785 full-length cDNAs coding for proteins containing 58-1536 amino acids. The v2.5 assembly was found to be of good quality based on validation using 200 full-length cDNAs from GenBank. Annotated isotigs from the reference transcriptome were attributable to 344 KEGG pathway maps. We identified 26 gene paralogues (20 of them teleost-specific) and 43 splice variants, of which 12 had functional domains missing that were likely to affect their biological function. Many key transcription factors, signaling molecules and structural proteins necessary for myogenesis and muscle growth have been identified. Physiological status affected the number of reads that mapped to isotigs, reflecting changes in gene expression between treatments. CONCLUSIONS: We have produced a comprehensive fast skeletal muscle transcriptome for the gilthead sea bream, which will provide a resource for SNP discovery in genes with a large effect on production traits of commercial interest and for expression studies of growth and adaptation.

• Genome wide response to dietary tetradecylthioacetic acid supplementation in the heart of Atlantic Salmon (Salmo salar L.).

  Authors: Fabian Grammes, Kjell-Arne Rørvik, Magny S Thomassen, Rolf K Berge, Harald Takle

  BMC genomics. 13(1):180.

  ABSTRACT: BACKGROUND: Under-dimensioned hearts causing functional problems are associated with higher mortality rates in intensiveAtlantic salmon aquaculture. Previous studies have indicated thatABSTRACT: BACKGROUND: Under-dimensioned hearts causing functional problems are associated with higher mortality rates in intensiveAtlantic salmon aquaculture. Previous studies have indicated that tetradecylthioacetic acid (TTA) induces cardiacgrowth and also stimulates transcription of peroxisome proliferator activated receptors (PPAR) ¿ and ß in theAtlantic salmon heart. Since cardiac and transcriptional responses to feed are of high interest in aquaculture, theobjective of this study was to characterize the transcriptional mechanisms induced by TTA in the heart of Atlanticsalmon. RESULTS: Atlantic salmon were kept at sea for 17 weeks. During the first 8 weeks the fish received a TTA supplementeddiet. Using microarrays, profound transcriptional effects were observed in the heart at the end of the experiment,9 weeks after the feeding of TTA stopped. Approximately 90% of the significant genes were expressed higher inthe TTA group. Hypergeometric testing revealed the over-representation of 35 gene ontology terms in the TTAfed group. The GO terms were generally categorized into cardiac performance, lipid catabolism, glycolysis andTCA cycle. CONCLUSIONS: Our results indicate that TTA has profound effects on cardiac performance based on results from microarray andqRT-PCR analysis. The gene expression profile favors a scenario of "physiological"lright hypertrophy recognizedby increased oxidative fatty acid metabolism, glycolysis and TCA cycle activity as well as cardiac growth andcontractility in the heart ventricle. Increased cardiac efficiency may offer significant benefits in the demandingAquaculture situations.

• The dependence of expression of NF-kappaB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR.

  Authors: Marta Iwanaszko, Allan R Brasier, Marek Kimmel

  BMC genomics. 13(1):182.

  ABSTRACT: BACKGROUND: The NF-kappaB family plays a prominent role in the innate immune response, cell cycle activation or cell apoptosis. Upon stimulation by pathogen-associated patterns, such asABSTRACT: BACKGROUND: The NF-kappaB family plays a prominent role in the innate immune response, cell cycle activation or cell apoptosis. Upon stimulation by pathogen-associated patterns, such as viral RNA a kinase cascade is activated, which strips the NF-kappaB of its inhibitor IkappaBalpha molecule and allows it to translocate into the nucleus. Once in the nucleus, it activates transcription of approximately 90 genes whose kinetics of expression differ relative to when NF-kappaB translocates into the nucleus, referred to as Early, Middle and Late genes. It is not obvious what mechanism is responsible for segregation of the genes' timing of transcriptional response. RESULTS: It is likely that the differences in timing are due, in part, to the number and type of transcription factor binding sites (TFBS), required for NF-kappaB itself as well as for the putative cofactors, in the Early versus Late genes. We therefore applied an evolutionary analysis of conserved TFBS. We also examined whether transcription dynamic was related to the presence of AU-rich elements (ARE) located in 3' UTR of the mRNA because recent studies have shown that the presence of AREs is associated with rapid gene induction. We found that Early genes were significantly enriched in NF-kappaB binding sites occurring in evolutionarily conserved domains compared to genes in the Late group. We also found that Early genes had significantly greater number of ARE sequences in the 3' UTR of the gene. The similarities observed among the Early genes were seen in comparison with distant species, while the Late genes promoter regions were much more diversified. Based on the promoter structure and ARE content, Middle genes can be divided into two subgroups which show similarities to Early and Late genes respectively. CONCLUSIONS: Our data suggests that the rapid response of the NF-kappaB dependent Early genes may be due to both increased gene transcription due to NF-kappaB loading as well as the contribution of mRNA instability to the transcript profiles. Wider phylogenetic analysis of NF-kappaB dependent genes provides insight into the degree of cross-species similarity found in the Early genes, opposed to many differences in promoter structure that can be found among the Late genes. These data suggest that activation and expression of the Late genes is much more species-specific than of the Early genes.

• Improving the performance of True Single Molecule Sequencing for ancient DNA.

  Authors: Aurelien Ginolhac, Julia Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant Zazula, Duane Froese, Kathleen E Steinmann, John F Thompson, Khaled As Al-Rasheid, Thomas Mp Gilbert, Eske Willerslev, Ludovic Orlando

  BMC genomics. 13(1):177.

  ABSTRACT: BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first completeABSTRACT: BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targetted.

• Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation.

  Authors: Tim Kahlke, Alexander Goesmann, Erik Hjerde, Nils Peder Willassen, Peik Haugen

  BMC genomics. 13(1):179.

  ABSTRACT: BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genomeABSTRACT: BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. RESULTS: The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. CONCLUSION: The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.

• Improving ancient DNA read mapping against modern reference genomes.

  Authors: Mikkel Schubert, Aurelien Ginolhac, Stinus Lindgreen, John F Thompson, Khaked As Al-Rasheid, Eske Willerslev, Anders Krogh, Ludovic Orlando

  BMC genomics. 13(1):178.

  ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species.ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.

• Construction of physical maps for the sex-specific regions of papaya sex chromosomes.

  Authors: Jong-Kuk Na, Jianping Wang, Jan E Murray, Andrea R Gschwend, Wenli Zhang, Qingyi Yu, Rafael Navajas-Perez, F Alex Feltus, Cuixia Chen, Zdenek Kubat, Paul H Moore, Jiming Jiang, Andrew H Paterson, Ray Ming

  BMC genomics. 13(1):176.

  ABSTRACT: BACKGROUND: Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination isABSTRACT: BACKGROUND: Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male), XYh (hermaphrodite), and XX (female). The papaya hermaphrodite-specific Yh chromosome region (HSY) is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement. RESULTS: A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC) libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89%) DNA sequence expansion. CONCLUSION: The 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2-3 million years ago. The genetically defined borders coincide with the common BACs on the minimum tiling paths of HSY and X. The minimum tiling paths of HSY and its X counterpart are being used for sequencing these X and Yh-specific regions.

• The footprint of metabolism in the organization of mammalian genomes.

  Authors: Luisa Berna, Ankita Chaurasia, Claudia Angelini, Concetta Federico, Salvatore Saccone, Giuseppe D'Onofrio

  BMC genomics. 13(1):174.

  ABSTRACT: BACKGROUND: At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biasedABSTRACT: BACKGROUND: At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes) according to the KOG database: (i) information storage and processing, (ii) cellular processes and signaling, and (iii) metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset. RESULTS: The GC3 level of the above functional categories was increasing from (i) to (iii). This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands. CONCLUSIONS: In the light of different evolutionary hypotheses proposed so far, and contributing with different potential to the genome compositional heterogeneity of mammalian genomes, the one based on the metabolic rate seems to play not a minor role. Keeping in mind similar results reported in bacteria and in teleosts, the specific compositional patterns observed in mammals highlight metabolic rate as unifying factor that fits over a wide range of living organisms.

• Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns.

  Authors: Vitthal T Barvkar, Varsha C Pardeshi, Sandip M Kale, Narendra Y Kadoo, Vidya S Gupta

  BMC genomics. 13(1):175.

  ABSTRACT: BACKGROUND: The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates variousABSTRACT: BACKGROUND: The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. RESULTS: Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged. CONCLUSIONS: Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.

• Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer.

  Authors: Jinnan Hu, Chenxi Chen, Tobin Peever, Ha Dang, Christopher Lawrence, Thomas Mitchell

  BMC genomics. 13(1):171.

  ABSTRACT: BACKGROUND: Fungal plant pathogens cause serious agricultural losses worldwide. Alternaria. arborescens is a major pathogen of tomato, with its virulence determined by the presence of aABSTRACT: BACKGROUND: Fungal plant pathogens cause serious agricultural losses worldwide. Alternaria. arborescens is a major pathogen of tomato, with its virulence determined by the presence of a conditionally dispensable chromosome (CDC) carrying host-specific toxin genes. Genes encoding these toxins are well-studied, however the genomic content and organization of the CDC is not known. RESULTS: To gain a richer understanding of the molecular determinants of virulence and the evolution of pathogenicity, we performed whole genome sequencing of A. arborescens. Here we present the de-novo assembly of the CDC and its predicted gene content. Also presented is hybridization data validating the CDC assembly. Predicted genes were functionally annotated through BLAST. Gene ontology terms were assigned, and conserved domains were identified. Differences in nucleotide usage were found between CDC genes and those on the essential chromosome (EC), including GC3-content, codon usage bias, and repeat region load. Genes carrying PKS and NRPS domains were identified in clusters on the CDC and evidence supporting the origin of the CDC through horizontal transfer from an unrelated fungus was found. CONCLUSIONS: We provide evidence supporting the hypothesis that the CDC in A. arborescens was acquired through horizontal transfer, likely from an unrelated fungus. We also identified several predicted CDC genes under positive selection that may serve as candidate virulence factors.

• Expansion of CORE-SINEs in the genome of the Tasmanian devil.

  Authors: Maria A Nilsson Janke, Axel Janke, Elizabeth P Murchison, Zemin Ning, Björn M Hallström

  BMC genomics. 13(1):172.

  ABSTRACT: BACKGROUND: The genome of the carnivorous marsupial, Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a betterABSTRACT: BACKGROUND: The genome of the carnivorous marsupial, Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious cancer devil facial tumor disease that is threatening the specie's survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. RESULTS: The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. CONCLUSIONS: The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

• Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection.

  Authors: Won Kyong Cho, Jisuk Yu, Kyung-Mi Lee, Moonil Son, Kyunghun Min, Yin-Won Lee, Kook-Hyung Kim

  BMC genomics. 13(1):173.

  ABSTRACT: BACKGROUND: Fusarium graminearum virus 1 strain DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causesABSTRACT: BACKGROUND: Fusarium graminearum virus 1 strain DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessary for preventing damage caused by F. graminearum. Therefore, we investigated important cellular regulatory processes in a host containing FgV1-DK21 as compared to an uninfected parent using a transcriptional approach. RESULTS: Using a 3' -tiling microarray covering all known F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum at two different time points. At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. In addition, genes required for transcription and signal transduction, including fungal-specific transcription factors and cAMP signaling, respectively, were actively up-regulated. In contrast, genes involved in various metabolic pathways, particularly in producing carboxylic acids, aromatic amino acids, nitrogen compounds, and polyamines, showed dramatic down-regulation at the early time point. Moreover, genes associated with transport systems localizing to transmembranes were down-regulated at both time points. CONCLUSION: This is the first report of global change in the prominent cellular pathways in the Fusarium host containing FgV1-DK21. The significant increase in transcripts for transcription and translation machinery in fungal host cells seems to be related to virus replication. In addition, significant down-regulation of genes required for metabolism and transporting systems in a fungal host containing the virus appears to be related to the host defense mechanism and fungal virulence. Taken together, our data aid in the understanding of how FgV1-DK21 regulates the transcriptional reprogramming of F. graminearum.

• GeSICA: Genome segmentation from intrachromosomal associations.

  Authors: Lin Liu, Yiqian Zhang, Jianxing Feng, Ning Zheng, Junfeng Yin, Yong Zhang

  BMC genomics. 13(1):164.

  ABSTRACT: BACKGROUND: Various aspects of genome organization have been explored based on data from distincttechnologies, including histone modification ChIP-Seq, 3C, and its derivatives.ABSTRACT: BACKGROUND: Various aspects of genome organization have been explored based on data from distincttechnologies, including histone modification ChIP-Seq, 3C, and its derivatives. Recentlydeveloped Hi-C techniques enable the genome wide mapping of DNA interactomes, therebyproviding the opportunity to study genome organization in detail, but these methods also posechallenges in methodology development. RESULTS: We developed Genome Segmentation from Intra Chromosomal Associations, or GeSICA, toexplore genome organization and applied the method to Hi-C data in human GM06990 andK562 cells. GeSICA calculates a simple logged ratio to efficiently segment the humangenome into regions with two distinct states that correspond to rich and poor functionalelement states. Inside the rich regions, Markov Clustering was subsequently applied tosegregate the regions into more detailed clusters. The binding sites of the insulator, cohesion,and transcription complexes are enriched in the boundaries between neighboring clusters,indicating that inferred clusters may have fine organizational features. CONCLUSIONS: Our study presents a novel analysis method, known as GeSICA, which gives insight intogenome organization based on Hi-C data. GeSICA is open source and freely available at:http://web.tongji.edu.cn/~zhanglab/GeSICA/

• AlliumMap-a comparative genomics resource for cultivated Allium vegetables.

  Authors: John A McCallum, Samantha Baldwin, Masayoshi Shigyo, Yanbo Deng, Sjaak van Heusden, Meeghan Pither-Joyce, Fernand Kenel

  BMC genomics. 13(1):168.

  ABSTRACT: BACKGROUND: Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepaABSTRACT: BACKGROUND: Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A. fistulosum and interspecific crosses between A. roylei and these two species, but it has not been possible to access genetic maps and underlying data from these studies easily. Description An online comparative genomics database, AlliumMap, has been developed based on the GMOD CMap tool at http://alliumgenetics.org. It has been populated with curated data linking genetic maps with underlying markers and sequence data from multiple studies. It includes data from multiple onion mapping populations as well as the most closely related species A. roylei and A. fistulosum. Further onion EST-derived markers were evaluated in the A. cepa x A. roylei interspecific population, enabling merging of the AFLP-based maps. In addition, data concerning markers assigned in multiple studies to the Allium physical map using A. cepa-A. fistulosum alien monosomic addition lines have been compiled. The compiled data reveal extensive synteny between onion and A. fistulosum. CONCLUSIONS: The database provides the first online resource providing genetic map and marker data from multiple Allium species and populations. The additional markers placed on the interspecific Allium map confirm the value of A. roylei as a valuable bridge between the genetics of onion and A. fistulosum and as a means to conduct efficient mapping of expressed sequence markers in Allium. The data presented suggest that comparative approaches will be valuable for genetic and genomic studies of onion and A. fistulosum. This online resource will provide a valuable means to integrate genetic and sequence-based explorations of Allium genomes.

• PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.

  Authors: Jumamurat R Bayjanov, Douwe Molenaar, Vesela Tzeneva, Roland J Siezen, Sacha Aft van Hijum

  BMC genomics. 13(1):170.

  ABSTRACT: BACKGROUND: Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype.ABSTRACT: BACKGROUND: Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances). Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. RESULTS: We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/) that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene) selection is based. Preprocessed data is used in feature (e.g., gene) selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value) to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. CONCLUSIONS: PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing), gene expression (determined by e.g.: microarrays or RNA-seq), or metabolite abundance (determined by e.g.: GC-MS).

• Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (macaca fascicularis) for biomedical research.

  Authors: Jae-Won Huh, Young-Hyun Kim, Sang-Je Park, Dae-Soo Kim, Sang-Rae Lee, Kyoung-Min Kim, Kang-Jin Jeong, Ji-Su Kim, Bong-Seok Song, Bo-Woong Sim, Sun-Uk Kim, Sang-Hyun Kim, Kyu-Tae Chang

  BMC genomics. 13(1):163.

  ABSTRACT: BACKGROUND: As a human mimic, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on thisABSTRACT: BACKGROUND: As a human mimic, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a significant obstacle for its broader use. RESULTS: Here, we sequenced the transcriptome of 16 tissues and identified genes to resolve the main obstacles for understanding the biological response of the crab-eating macaque. From 4 million reads with 1.4 billion base sequences, 31,786 isotigs containing genes similar to those of humans, 12,672 novel isotigs, and 348,160 singletons were identified using the GS FLX sequencing method. Approximately 86% of human genes were represented among the genes sequenced in this study. Additionally, 175 tissue-specific genes were identified, 81 of which were experimentally validated. In total, 4,314 alternative splicing (AS) events were identified and analyzed. Intriguingly, 10.4% of AS events were associated with transposable element (TE) insertions. Finally, investigation of TE exonization events and evolutionary analysis were conducted, revealing interesting phenomena of human-specific amplified trends in TE exonization events. CONCLUSIONS: This report represents the first large-scale transcriptome sequencing and genetic analyses of M. fascicularis and could contribute to its utility for biomedical research and basic biology.

• A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T.

  Authors: Shivakumara Siddaramappa, Jean F Challacombe, Rosana E De Castro, Friedhelm Pfeiffer, Diego E Sastre, María I Giménez, Roberto A Paggi, John C Detter, Karen W Davenport, Lynne A Goodwin, Nikolaos Kyrpides, Roxanne Tapia, Samuel Pitluck, Susan Lucas, Tanja Woyke, Julie A Maupin-Furlow

  BMC genomics. 13(1):165.

  ABSTRACT: BACKGROUND: Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is adual extremophile requiring alkaline conditions and hypersalinity for optimal growth.ABSTRACT: BACKGROUND: Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is adual extremophile requiring alkaline conditions and hypersalinity for optimal growth. Thegenome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain acomprehensive insight into the genetic content of this haloarchaeon and to understand thebasis of some of the cellular functions necessary for its survival. RESULTS: The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bpand encodes 4,212 putative proteins, some of which contain peptide repeats of variouslengths. Comparative genome analyses facilitated the identification of genes encodingputative proteins involved in adaptation to hypersalinity, stress response, glycosylation, andpolysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putativecytochromes and other proteins supporting aerobic respiration and electron transfer wereencoded by one or more of Nab. magadii replicons. The genome encodes a number ofputative proteases/peptidases as well as protein secretion functions. Genes encoding putativetranscriptional regulators, basal transcription factors, signal perception/transduction proteins,and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for thebiosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential cofactorswere deduced by in depth sequence analyses. However, approximately 36% of Nab.magadii protein coding genes could not be assigned a function based on blast analysis andhave been annotated as encoding hypothetical or conserved hypothetical proteins.Furthermore, despite extensive comparative genomic analyses, genes necessary for survivalin alkaline conditions could not be identified in Nab. magadii. CONCLUSIONS: Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and itcould use different carbon and energy sources to sustain growth. Nab. magadii has thegenetic potential to adapt to its milieu by intracellular accumulation of inorganic cationsand/or neutral organic compounds. The identification of Nab. magadii genes involved incoenzyme biosynthesis is a necessary step toward further reconstruction of the metabolicpathways in halophilic archaea and other extremophiles. The knowledge gained from thegenome sequence of this haloalkaliphilic archaeon is highly valuable in advancing theapplications of extremophiles and their enzymes.

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