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Ashlee M Earl,
Christopher A Desjardins, Michael G Fitzgerald,
Harindra M Arachchi,
Qiandong Zeng,
Teena Mehta,
Allison Griggs,
Bruce W Birren,
Nadege C Toney,
Janice Carr,
James Posey,
W Ray Butler
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ABSTRACT: Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon-chain length mycolic acids bound in the cell wall. S. rugosus is also a medically important species because it is an opportunistic pathogen associated with mammalian lung disease. This report represents the second species in the genus to have its genome sequenced. The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part of the NIH Roadmap for Medical Research, Human Microbiome Project.
Standards in Genomic Sciences 12/2011; 5(3):389-97. · 1.62 Impact Factor
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Nicholas Rhind,
Zehua Chen,
Moran Yassour,
Dawn A Thompson,
Brian J Haas,
Naomi Habib,
Ilan Wapinski,
Sushmita Roy,
Michael F Lin,
David I Heiman, [......],
Hanah Margalit,
Rob Martienssen,
Conrad A Nieduszynski,
Joseph W Spatafora,
Nir Friedman,
Jacob Z Dalgaard,
Peter Baumann,
Hironori Niki,
Aviv Regev,
Chad Nusbaum
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ABSTRACT: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
Science 05/2011; 332(6032):930-6. · 31.20 Impact Factor
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Karen E Nelson,
George M Weinstock,
Sarah K Highlander,
Kim C Worley,
Heather Huot Creasy,
Jennifer Russo Wortman,
Douglas B Rusch,
Makedonka Mitreva,
Erica Sodergren,
Asif T Chinwalla, [......],
Sandra W Clifton,
Emma Allen-Vercoe,
Ashlee M Earl,
Candace N Farmer,
Konstantinos Liolios,
Michael G Surette,
Qiang Xu,
Craig Pohl,
Katarzyna Wilczek-Boney,
Dianhui Zhu
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ABSTRACT: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
Science 05/2010; 328(5981):994-9. · 31.20 Impact Factor
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Michael C Zody,
Manuel Garber,
Ted Sharpe,
Sarah K Young,
Lee Rowen,
Keith O'Neill,
Charles A Whittaker,
Michael Kamal,
Jean L Chang,
Christina A Cuomo, [......],
Carrie Sougnez,
Sabrina M Stone,
Kerri Topham,
Dascena Vincent,
Shunguang Wang,
Andrew R Zimmer,
Bruce W Birren,
Leroy Hood,
Eric S Lander,
Chad Nusbaum
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ABSTRACT: Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.
Nature 04/2006; 440(7084):671-5. · 36.28 Impact Factor
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Todd D Taylor,
Hideki Noguchi,
Yasushi Totoki,
Atsushi Toyoda,
Yoko Kuroki,
Ken Dewar,
Christine Lloyd,
Takehiko Itoh,
Tadayuki Takeda,
Dae-Won Kim, [......],
Xiaoping Yang,
Andrew R Zimmer,
Michael C Zody,
Bruce W Birren,
Chad Nusbaum,
Asao Fujiyama,
Masahira Hattori,
Jane Rogers,
Eric S Lander,
Yoshiyuki Sakaki
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ABSTRACT: Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
Nature 04/2006; 440(7083):497-500. · 36.28 Impact Factor
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Michael C. Zody,
Manuel Garber,
Ted Sharpe,
Sarah K. Young,
Lee Rowen,
Keith O'Neill,
Charles A. Whittaker,
Michael Kamal,
Jean L. Chang,
Christina A. Cuomo, [......],
Carrie Sougnez,
Sabrina M. Stone,
Kerri Topham,
Dascena Vincent,
Shunguang Wang,
Andrew R. Zimmer,
Bruce W. Birren,
Leroy Hood,
Eric S. Lander,
Chad Nusbaum
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ABSTRACT: Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication
Nature 03/2006; 440(7084):671-675. · 36.28 Impact Factor
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Chad Nusbaum,
Tarjei S Mikkelsen,
Michael C Zody,
Shuichi Asakawa,
Stefan Taudien,
Manuel Garber,
Chinnappa D Kodira,
Mary G Schueler,
Atsushi Shimizu,
Charles A Whittaker, [......],
Gaiping Wen,
Satoru Yamazaki,
Sarah K Young,
Qiandong Zeng,
Andrew R Zimmer,
Andre Rosenthal,
Bruce W Birren,
Matthias Platzer,
Nobuyoshi Shimizu,
Eric S Lander
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ABSTRACT: The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.
Nature 02/2006; 439(7074):331-5. · 36.28 Impact Factor
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Chad Nusbaum,
Tarjei S. Mikkelsen,
Michael C. Zody,
Shuichi Asakawa,
Stefan Taudien,
Manuel Garber,
Chinnappa D. Kodira,
Mary G. Schueler,
Atsushi Shimizu,
Charles A. Whittaker, [......],
Gaiping Wen,
Satoru Yamazaki,
Sarah K. Young,
Qiandong Zeng,
Andrew R. Zimmer,
Andre Rosenthal,
Bruce W. Birren,
Matthias Platzer,
Nobuyoshi Shimizu,
Eric S. Lander
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ABSTRACT: The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome
Nature 01/2006; 439(7074):331-335. · 36.28 Impact Factor
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Chad Nusbaum,
Michael C. Zody,
Mark L. Borowsky,
Michael Kamal,
Chinnappa D. Kodira,
Todd D. Taylor,
Charles A. Whittaker,
Jean L. Chang,
Christina A. Cuomo,
Ken Dewar, [......],
Atsushi Toyoda,
Hester M. Wain,
Sarah K. Young,
Qiandong Zeng,
Andrew R. Zimmer,
Asao Fujiyama,
Masahira Hattori,
Bruce W. Birren,
Yoshiyuki Sakaki,
Eric S. Lander
Nature 11/2005; 438(7068):696-696. · 36.28 Impact Factor
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Chad Nusbaum,
Michael C Zody,
Mark L Borowsky,
Michael Kamal,
Chinnappa D Kodira,
Todd D Taylor,
Charles A Whittaker,
Jean L Chang,
Christina A Cuomo,
Ken Dewar, [......],
Atsushi Toyoda,
Hester M Wain,
Sarah K Young,
Qiandong Zeng,
Andrew R Zimmer,
Asao Fujiyama,
Masahira Hattori,
Bruce W Birren,
Yoshiyuki Sakaki,
Eric S Lander
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ABSTRACT: Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
Nature 10/2005; 437(7058):551-5. · 36.28 Impact Factor
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Chad Nusbaum,
Michael C. Zody,
Mark L. Borowsky,
Michael Kamal,
Chinnappa D. Kodira,
Todd D. Taylor,
Charles A. Whittaker,
Jean L. Chang,
Christina A. Cuomo,
Ken Dewar, [......],
Atsushi Toyoda,
Hester M. Wain,
Sarah K. Young,
Qiandong Zeng,
Andrew R. Zimmer,
Asao Fujiyama,
Masahira Hattori,
Bruce W. Birren,
Yoshiyuki Sakaki,
Eric S. Lander
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ABSTRACT: Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term
Nature 09/2005; 437(7058):551-555. · 36.28 Impact Factor
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Jacob D Jaffe,
Nicole Stange-Thomann,
Cherylyn Smith,
David DeCaprio,
Sheila Fisher,
Jonathan Butler,
Sarah Calvo,
Tim Elkins, Michael G FitzGerald,
Nabil Hafez,
Chinnappa D Kodira,
John Major,
Shunguang Wang,
Jane Wilkinson,
Robert Nicol,
Chad Nusbaum,
Bruce Birren,
Howard C Berg,
George M Church
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ABSTRACT: Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.
Genome Research 09/2004; 14(8):1447-61. · 13.61 Impact Factor
