Jeremy Schmutz

Publications (97)1672.38 Total impact

• Article: Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).

  Ji-Yi Zhang, Yi-Ching Lee, Ivone Torres-Jerez, Mingyi Wang, Yanbin Yin, Wen-Chi Chou, Ji He, Hui Shen, Avinash C Srivastava, Christa Pennacchio, [......], Jeremy Schmutz, Ying Xu, Manoj Sharma, Rita Sharma, Laura E Bartley, Pamela C Ronald, Malay C Saha, Richard A Dixon, Yuhong Tang, Michael K Udvardi
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  ABSTRACT: Switchgrass (P. virgatum L.) is a perennial C4 grass with potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology and an additional 169,079 Sanger sequences were obtained from the 5' and 3' ends of 93,312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77,854 and 30,524 unique transcripts (unitranscripts), respectively, using the Newbler and PAVE programs. Published Sanger-ESTs (544,225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128,058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122,973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid-monolignol biosynthesis pathway. © 2013 The Authors. The Plant Journal © 2013 Blackwell Publishing Ltd.
  The Plant Journal 01/2013; · 6.16 Impact Factor
• Article: Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens.

  Bradford J Condon, Yueqiang Leng, Dongliang Wu, Kathryn E Bushley, Robin A Ohm, Robert Otillar, Joel Martin, Wendy Schackwitz, Jane Grimwood, Nurainizzati Mohdzainudin, [......], James Han, Alex Copeland, Erika Lindquist, Kerrie Barry, Jeremy Schmutz, Scott E Baker, Lynda M Ciuffetti, Igor V Grigoriev, Shaobin Zhong, B Gillian Turgeon
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  ABSTRACT: The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
  PLoS Genetics 01/2013; 9(1):e1003233. · 8.69 Impact Factor
• Article: The Reference Genome of the Halophytic Plant Eutrema salsugineum.

  Ruolin Yang, David E Jarvis, Hao Chen, Mark A Beilstein, Jane Grimwood, Jerry Jenkins, Shengqiang Shu, Simon Prochnik, Mingming Xin, Chuang Ma, Jeremy Schmutz, Rod A Wing, Thomas Mitchell-Olds, Karen S Schumaker, Xiangfeng Wang
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  ABSTRACT: Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8× coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.
  Frontiers in plant science. 01/2013; 4:46.
• Source

  Available from: Jianchang Du

  Dataset: nature08670

  Gregory D May, Gary Stacey, Randy C Shoemaker, Jianchang Du, Uffe Hellsten, Dong Xu, Dan Rokhsar, Brian Abernathy, Montona Futrell-Griggs, Jianlin Cheng, [......], Jeremy Schmutz, Madan K Bhattacharyya, Trupti Joshi, Taishi Umezawa, Navdeep Gill, Tetsuya Sakurai, Liucun Zhu, Yeisoo Yu, Zhixi Tian, Scott A Jackson
• Article: Identical Genomic Organization of Two Hemichordate Hox Clusters.

  Robert Freeman, Tetsuro Ikuta, Michael Wu, Ryo Koyanagi, Takeshi Kawashima, Kunifumi Tagawa, Tom Humphreys, Guang-Chen Fang, Asao Fujiyama, Hidetoshi Saiga, Christopher Lowe, Kim Worley, Jerry Jenkins, Jeremy Schmutz, Marc Kirschner, Daniel Rokhsar, Nori Satoh, John Gerhart
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  ABSTRACT: Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor [1-5]. Because hox genes play pivotal developmental roles in bilaterian animals [6-8], we analyzed the Hox complexes of two hemichordate genomes. We find that Saccoglossus kowalevskii and Ptychodera flava both possess 12-gene clusters, with mir10 between hox4 and hox5, in 550 kb and 452 kb intervals, respectively. Genes hox1-hox9/10 of the clusters are in the same genomic order and transcriptional orientation as their orthologs in chordates, with hox1 at the 3' end of the cluster. At the 5' end, each cluster contains three posterior genes specific to Ambulacraria (the hemichordate-echinoderm clade), two forming an inverted terminal pair. In contrast, the echinoderm Strongylocentrotus purpuratus contains a 588 kb cluster [9] of 11 orthologs of the hemichordate genes, ordered differently, plausibly reflecting rearrangements of an ancestral hemichordate-like ambulacrarian cluster. Hox clusters of vertebrates and the basal chordate amphioxus [10] have similar organization to the hemichordate cluster, but with different posterior genes. These results provide genomic evidence for a well-ordered complex in the deuterostome ancestor for the hox1-hox9/10 region, with the number and kind of posterior genes still to be elucidated.
  Current biology: CB 10/2012; · 10.99 Impact Factor
• Source

  Available from: Francis Michel Martin

  Article: Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.

  Emmanuelle Morin, Annegret Kohler, Adam R Baker, Marie Foulongne-Oriol, Vincent Lombard, Laszlo G Nagy, Robin A Ohm, Aleksandrina Patyshakuliyeva, Annick Brun, Andrea L Aerts, [......], Dan Cullen, Ronald P de Vries, Taina Lundell, David S Hibbett, Bernard Henrissat, Kerry S Burton, Richard W Kerrigan, Michael P Challen, Igor V Grigoriev, Francis Martin
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  ABSTRACT: Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
  Proceedings of the National Academy of Sciences 10/2012; 109(43):17501-6. · 9.68 Impact Factor
• Article: Theria-Specific Homeodomain and cis-Regulatory Element Evolution of the Dlx3-4 Bigene Cluster in 12 Different Mammalian Species.

  Kenta Sumiyama, Tsutomu Miyake, Jane Grimwood, Andrew Stuart, Mark Dickson, Jeremy Schmutz, Frank H Ruddle, Richard M Myers, Chris T Amemiya
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  ABSTRACT: The mammalian Dlx3 and Dlx4 genes are configured as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that largely reside within the intergenic region of the cluster. Previous work revealed that there are conspicuously conserved elements within the intergenic region of the Dlx3-4 bigene clusters of mouse and human. In this paper we have extended these analyses to include 12 additional mammalian taxa (including a marsupial and a monotreme) in order to better define the nature and molecular evolutionary trends of the coding and non-coding functional elements among morphologically divergent mammals. Dlx3-4 regions were fully sequenced from 12 divergent taxa of interest. We identified three theria-specific amino acid replacements in homeodomain of Dlx4 gene that functions in placenta. Sequence analyses of constrained nucleotide sites in the intergenic non-coding region showed that many of the intergenic conserved elements are highly conserved and have evolved slowly within the mammals. In contrast, a branchial arch/craniofacial enhancer I37-2 exhibited accelerated evolution at the branch between the monotreme and therian common ancestor despite being highly conserved among therian species. Functional analysis of I37-2 in transgenic mice has shown that the equivalent region of the platypus fails to drive transcriptional activity in branchial arches. These observations, taken together with our molecular evolutionary data, suggest that theria-specific episodic changes in the I37-2 element may have contributed to craniofacial innovation at the base of the mammalian lineage. J. Exp. Zool. (Mol. Dev. Evol.) 9999B:1-12, 2012. © 2012 Wiley Periodicals, Inc.
  Journal of Experimental Zoology Part B Molecular and Developmental Evolution 09/2012; · 2.42 Impact Factor
• Article: Genetic architecture of variation in the lateral line sensory system of threespine sticklebacks.

  Abigail R Wark, Margaret G Mills, Lam-Ha Dang, Yingguang Frank Chan, Felicity C Jones, Shannon D Brady, Devin M Absher, Jane Grimwood, Jeremy Schmutz, Richard M Myers, David M Kingsley, Catherine L Peichel
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  ABSTRACT: Vertebrate sensory systems have evolved remarkable diversity, but little is known about the underlying genetic mechanisms. The lateral line sensory system of aquatic vertebrates is a promising model for genetic investigations of sensory evolution because there is extensive variation within and between species, and this variation is easily quantified. In the present study, we compare the lateral line sensory system of threespine sticklebacks (Gasterosteus aculeatus) from an ancestral marine and a derived benthic lake population. We show that lab-raised individuals from these populations display differences in sensory neuromast number, neuromast patterning, and groove morphology. Using genetic linkage mapping, we identify regions of the genome that influence different aspects of lateral line morphology. Distinct loci independently affect neuromast number on different body regions, suggesting that a modular genetic structure underlies the evolution of peripheral receptor number in this sensory system. Pleiotropy and/or tight linkage are also important, as we identify a region on linkage group 21 that affects multiple aspects of lateral line morphology. Finally, we detect epistasis between a locus on linkage group 4 and a locus on linkage group 21; interactions between these loci contribute to variation in neuromast pattern. Our results reveal a complex genetic architecture underlying the evolution of the stickleback lateral line sensory system. This study further uncovers a genetic relationship between sensory morphology and non-neural traits (bony lateral plates), creating an opportunity to investigate morphological constraints on sensory evolution in a vertebrate model system.
  G3 (Bethesda, Md.). 09/2012; 2(9):1047-56.
• Source

  Available from: Micaela Schnitzler Parker

  Dataset: Worden et al Micromonas Supplementary Materials

  Alexandra Z Worden, Jae-Hyeok Lee, Thomas Mock, Pierre Rouzé, Melinda P Simmons, Andrea L Aerts, Andrew E Allen, Marie L Cuvelier, Evelyne Derelle, Meredith V Everett, [......], Jeremy Schmutz, Eve Toulza, Tania Wyss, Alexander Zelensky, Kemin Zhou, E Virginia Armbrust, Debashish Bhattacharya, Ursula W. Goodenough, Yves Van de Peer, Igor V Grigoriev
• Source

  Available from: Francis Michel Martin

  Article: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.

  Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A Blanchette, Bernard Henrissat, Angel T Martínez, Robert Otillar, Joseph W Spatafora, Jagjit S Yadav, [......], Khajamohiddin Syed, Adrian Tsang, Ad Wiebenga, Darcy Young, Antonio Pisabarro, Daniel C Eastwood, Francis Martin, Dan Cullen, Igor V Grigoriev, David S Hibbett
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  ABSTRACT: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
  Science 06/2012; 336(6089):1715-9. · 31.20 Impact Factor
• Article: The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

  Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Otillar, Joseph W. Spatafora, Jagjit S. Yadav, [......], Khajamohiddin Syed, Adrian Tsang, Ad Wiebenga, Darcy Young, Antonio Pisabarro, Daniel C. Eastwood, Francis Martin, Dan Cullen, Igor V. Grigoriev, David S. Hibbett
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  ABSTRACT: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
  Science 06/2012; 336(10.1126/science.1221748):1715-1719. · 31.20 Impact Factor
• Article: The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

  Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D. Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, [......], Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten
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  ABSTRACT: Background Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Results The 48.8-Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes was highly reshuffled within synteny blocks suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C- 169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN). Conclusions We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.
  Genome Biology 05/2012; 13(R39). · 9.04 Impact Factor
• Article: The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.

  Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, [......], Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten
  [show abstract] [hide abstract]
  ABSTRACT: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN). We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.
  Genome biology 05/2012; 13(5):R39. · 6.63 Impact Factor
• Source

  Available from: Xiaomei Wu

  Article: Reference genome sequence of the model plant Setaria.

  Jeffrey L Bennetzen, Jeremy Schmutz, Hao Wang, Ryan Percifield, Jennifer Hawkins, Ana C Pontaroli, Matt Estep, Liang Feng, Justin N Vaughn, Jane Grimwood, [......], Manoj Sharma, Rita Sharma, Pamela C Ronald, Olivier Panaud, Elizabeth A Kellogg, Thomas P Brutnell, Andrew N Doust, Gerald A Tuskan, Daniel Rokhsar, Katrien M Devos
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  ABSTRACT: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
  Nature Biotechnology 05/2012; 30(6):555-61. · 29.50 Impact Factor
• Article: The genomic basis of adaptive evolution in threespine sticklebacks.

  Felicity C Jones, Manfred G Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C Zody, Simon White, [......], Chris Amemiya, Jen Baldwin, Toby Bloom, David B Jaffe, Robert Nicol, Jane Wilkinson, Eric S Lander, Federica Di Palma, Kerstin Lindblad-Toh, David M Kingsley
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  ABSTRACT: Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
  Nature 04/2012; 484(7392):55-61. · 36.28 Impact Factor
• Article: The genomic basis of adaptive evolution in threespine sticklebacks

  Felicity C. Jones, Manfred G. Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C. Zody, Simon White, [......], Haili Zhang, Alex A. Pollen, Timothy Howes, Chris Amemiya, Broad Institute Genome Sequencing Platform, Whole Genome Assembly Team, Eric S. Lander, Federica Di Palma, Kerstin Lindblad-Toh, David M. Kingsley
  [show abstract] [hide abstract]
  ABSTRACT: Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
  Nature. 04/2012; 484(7392):55-61.
• Article: The genomic basis of adaptive evolution in threespine sticklebacks

  Felicity C Jones, Manfred G Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C Zody, Simon White, [......], Chris Amemiya, Jen Baldwin, Toby Bloom, David B Jaffe, Robert Nicol, Jane Wilkinson, Eric S Lander, Federica Di Palma, Kerstin Lindblad-Toh, David M Kingsley
  [show abstract] [hide abstract]
  ABSTRACT: Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
  Nature 04/2012; 484(7392):55-61. · 36.28 Impact Factor
• Source

  Available from: Francis Michel Martin

  Article: Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.

  Ake Olson, Andrea Aerts, Fred Asiegbu, Lassaad Belbahri, Ourdia Bouzid, Anders Broberg, Björn Canbäck, Pedro M Coutinho, Dan Cullen, Kerstin Dalman, [......], Jerry Ståhlberg, Heriberto Vélëz, Ronald P de Vries, Ad Wiebenga, Steve Woodward, Igor Yakovlev, Matteo Garbelotto, Francis Martin, Igor V Grigoriev, Jan Stenlid
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  ABSTRACT: Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.
  New Phytologist 03/2012; 194(4):1001-13. · 6.64 Impact Factor
• Source

  Available from: Qinglong L Wu

  Article: Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).

  Linda Meincke, Alex Copeland, Alla Lapidus, Susan Lucas, Kerrie W Berry, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice, Sam Pitluck, [......], Miriam Land, Loren Hauser, Nikos C Kyrpides, Natalia Ivanova, Markus Göker, Tanja Woyke, Qinglong L Wu, Matthias Pöckl, Martin W Hahn, Hans-Peter Klenk
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  ABSTRACT: Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.
  Standards in Genomic Sciences 03/2012; 6(1):74-83. · 1.62 Impact Factor
• Source

  Available from: Manoj K Sharma

  Article: A genome-wide survey of switchgrass genome structure and organization.

  Manoj K Sharma, Rita Sharma, Peijian Cao, Jerry Jenkins, Laura E Bartley, Morgan Qualls, Jane Grimwood, Jeremy Schmutz, Daniel Rokhsar, Pamela C Ronald
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  ABSTRACT: The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
  PLoS ONE 01/2012; 7(4):e33892. · 4.09 Impact Factor