Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny
LaDeana W. Hillier,Raymond D. Miller,Scott Everet Baird,Asif T. Chinwalla,Lucinda Fulton,Daniel C. Koboldt,Robert H. Waterston +6 more
Reads0
Chats0
TLDR
The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that is only poorly understood presently.Abstract:
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C briggsae chromosomes Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse We found that, like C elegans chromosomes, C briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presentlyread more
Citations
More filters
Journal ArticleDOI
Genomic signatures of selection at linked sites: unifying the disparity among species
Asher D. Cutter,Bret A. Payseur +1 more
TL;DR: The dominant features that could drive differences in linked selection among species are characterized — including roles for selective sweeps being 'hard' or 'soft' — and the concealing effects of demography and confounding genomic variables are characterized.
Book
Sex Chromosomes and Sex-Linked Genes
TL;DR: Evidence is provided that the X and the Y or the Z and the W were Originally an Homologous Pair of Ordinary Chromosomes, and the Conservation of the Original X or Z.
Journal ArticleDOI
Dispersal and gene flow in free-living marine nematodes
TL;DR: In this paper, the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart is discussed. And the authors discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity.
Journal ArticleDOI
Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis
TL;DR: This review describes how holocentricity may be identified through cytological and molecular methods and how extensive genome sequencing and experiments in nonmodel organisms may allow Holocentric chromosomes to shed light on general principles of chromosome segregation.
Journal ArticleDOI
Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate
TL;DR: Divergence times are inferred among 6 species each of Caenorhabditis and Drosophila, based on thousands of orthologous groups of genes, and direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection are illustrated.
References
More filters
Book ChapterDOI
Primer3 on the WWW for general users and for biologist programmers.
Steve Rozen,Helen Skaletsky +1 more
TL;DR: This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Initial sequencing and comparative analysis of the mouse genome.
Robert H. Waterston,Kerstin Lindblad-Toh,Ewan Birney,Jane Rogers,Josep F. Abril,Pankaj K. Agarwal,Richa Agarwala,Rachel Ainscough,Marina Alexandersson,Peter An,Stylianos E. Antonarakis,John Attwood,Robert Baertsch,J Bailey,K F Barlow,Stephan Beck,Eric Berry,Bruce W. Birren,Toby Bloom,Peer Bork,Marc Botcherby,Nicolas Bray,Michael R. Brent,Daniel G. Brown,Daniel G. Brown,Stephen D. Brown,Carol J. Bult,John Burton,Jonathan Butler,R. D. Campbell,Piero Carninci,Simon Cawley,Francesca Chiaromonte,Asif T. Chinwalla,Deanna M. Church,Michele Clamp,C M Clee,Francis S. Collins,Lisa Cook,Richard R. Copley,Alan Coulson,Olivier Couronne,James Cuff,Val Curwen,Tim Cutts,Mark J. Daly,Robert David,Joy Davies,Kimberly D. Delehaunty,Justin Deri,Emmanouil T. Dermitzakis,Colin N. Dewey,Nicholas J. Dickens,Mark Diekhans,Sheila Dodge,Inna Dubchak,Diane M. Dunn,Sean R. Eddy,Laura Elnitski,Richard D. Emes,Pallavi Eswara,Eduardo Eyras,Adam Felsenfeld,Ginger A. Fewell,Paul Flicek,Karen Foley,Wayne N. Frankel,Lucinda Fulton,Robert S. Fulton,Terrence S. Furey,Diane Gage,Richard A. Gibbs,Gustavo Glusman,Sante Gnerre,Nick Goldman,Leo Goodstadt,Darren Grafham,Tina Graves,Eric D. Green,Simon G. Gregory,Roderic Guigó,Mark S. Guyer,Ross C. Hardison,David Haussler,Yoshihide Hayashizaki,Deana W. LaHillier,Angela S. Hinrichs,Wratko Hlavina,Timothy Holzer,Fan Hsu,Axin Hua,Tim Hubbard,Adrienne Hunt,Ian J. Jackson,David B. Jaffe,L. Steven Johnson,Matthew Jones,Thomas A. Jones,A Joy,Michael Kamal,Elinor K. Karlsson,Donna Karolchik,Arkadiusz Kasprzyk,Jun Kawai,Evan Keibler,Cristyn Kells,W. James Kent,Andrew Kirby,Diana L. Kolbe,Ian F Korf,Raju Kucherlapati,Edward J. Kulbokas,David Kulp,Tom Landers,J. P. Leger,Steven Leonard,Ivica Letunic,Rosie Levine,Jia Li,Ming Li,Christine Lloyd,Susan Lucas,Bin Ma,Donna Maglott,Elaine R. Mardis,Lucy Matthews,Evan Mauceli,John Mayer,Megan McCarthy,W. Richard McCombie,Stuart McLaren,Kirsten McLay,John Douglas Mcpherson,James Meldrim,Beverley Meredith,Jill P. Mesirov,Webb Miller,Tracie L. Miner,Emmanuel Mongin,Kate Montgomery,Michael J. Morgan,Richard Mott,James C. Mullikin,Donna M. Muzny,William E. Nash,Joanne O. Nelson,Michael N. Nhan,Robert Nicol,Zemin Ning,Chad Nusbaum,Michael J. O’Connor,Yasushi Okazaki,Karen Oliver,Emma Overton-Larty,Lior Pachter,Genís Parra,Kymberlie H. Pepin,Jane Peterson,Pavel A. Pevzner,Robert W. Plumb,Craig Pohl,Alex Poliakov,Tracy C. Ponce,Chris P. Ponting,Simon C. Potter,Michael A. Quail,Alexandre Reymond,Bruce A. Roe,Krishna M. Roskin,Edward M. Rubin,Alistair G. Rust,Ralph Santos,Victor Sapojnikov,Brian Schultz,Jörg Schultz,Matthias S. Schwartz,Scott Schwartz,Carol Scott,Steven Seaman,Steve Searle,Ted Sharpe,Andrew Sheridan,Ratna Shownkeen,Sarah Sims,Jonathan Singer,Guy Slater,Arian F.A. Smit,Douglas Smith,Brian Spencer,Arne Stabenau,Nicole Stange-Thomann,Charles W. Sugnet,Mikita Suyama,Glenn Tesler,Johanna Thompson,David Torrents,Evanne Trevaskis,John Tromp,Catherine Ucla,Abel Ureta-Vidal,Jade P. Vinson,Andrew von Niederhausern,Claire M. Wade,Melanie M. Wall,R. J. Weber,Robert B. Weiss,Michael C. Wendl,Anthony P. West,Kris A. Wetterstrand,Raymond Wheeler,Simon Whelan,Jamey Wierzbowski,David Willey,Sophie Williams,Richard K. Wilson,Eitan E. Winter,Kim C. Worley,Dudley Wyman,Shan Yang,Shiaw Pyng Yang,Evgeny M. Zdobnov,Michael C. Zody,Eric S. Lander +222 more
TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
Journal ArticleDOI
Finishing the euchromatic sequence of the human genome
Chris P. Ponting,Daniel Barker +1 more
TL;DR: The current human genome sequence (Build 35) as discussed by the authors contains 2.85 billion nucleotides interrupted by only 341 gaps and is accurate to an error rate of approximately 1 event per 100,000 bases.
Related Papers (5)
The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics
Lincoln Stein,Zhirong Bao,Zhirong Bao,Darin Blasiar,Thomas Blumenthal,Michael R. Brent,Nansheng Chen,Asif T. Chinwalla,Laura Clarke,Chris Clee,Avril Coghlan,Alan Coulson,Alan Coulson,Peter D'Eustachio,Peter D'Eustachio,David H. A. Fitch,Lucinda Fulton,Robert E Fulton,Sam Griffiths-Jones,Todd W. Harris,LaDeana W. Hillier,LaDeana W. Hillier,Ravi Kamath,Patricia E. Kuwabara,Elaine R. Mardis,Marco A. Marra,Marco A. Marra,Tracie L. Miner,Patrick Minx,James C. Mullikin,James C. Mullikin,Robert W. Plumb,Jane Rogers,Jacqueline E. Schein,Jacqueline E. Schein,Marc Sohrmann,John Spieth,Jason E. Stajich,Chaochun Wei,David Willey,Richard K. Wilson,Richard Durbin,Robert H. Waterston,Robert H. Waterston +43 more