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1.  Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster 
Nature genetics  2011;43(12):1179-1185.
Many animal species use a chromosome-based mechanism of sex determination, which has led to the coordinate evolution of dosage-compensation systems. Dosage compensation not only corrects the imbalance in the number of X chromosomes between the sexes but also is hypothesized to correct dosage imbalance within cells that is due to monoallelic X-linked expression and biallelic autosomal expression, by upregulating X-linked genes twofold (termed ‘Ohno’s hypothesis’). Although this hypothesis is well supported by expression analyses of individual X-linked genes and by microarray-based transcriptome analyses, it was challenged by a recent study using RNA sequencing and proteomics. We obtained new, independent RNA-seq data, measured RNA polymerase distribution and reanalyzed published expression data in mammals, C. elegans and Drosophila. Our analyses, which take into account the skewed gene content of the X chromosome, support the hypothesis of upregulation of expressed X-linked genes to balance expression of the genome.
doi:10.1038/ng.948
PMCID: PMC3576853  PMID: 22019781
2.  Insights into hominid evolution from the gorilla genome sequence 
Nature  2012;483(7388):169-175.
Summary
Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.
doi:10.1038/nature10842
PMCID: PMC3303130  PMID: 22398555
3.  The genome of a songbird 
Warren, Wesley C. | Clayton, David F. | Ellegren, Hans | Arnold, Arthur P. | Hillier, LaDeana W. | Künstner, Axel | Searle, Steve | White, Simon | Vilella, Albert J. | Fairley, Susan | Heger, Andreas | Kong, Lesheng | Ponting, Chris P. | Jarvis, Erich D. | Mello, Claudio V. | Minx, Pat | Lovell, Peter | Velho, Tarciso A. F. | Ferris, Margaret | Balakrishnan, Christopher N. | Sinha, Saurabh | Blatti, Charles | London, Sarah E. | Li, Yun | Lin, Ya-Chi | George, Julia | Sweedler, Jonathan | Southey, Bruce | Gunaratne, Preethi | Watson, Michael | Nam, Kiwoong | Backström, Niclas | Smeds, Linnea | Nabholz, Benoit | Itoh, Yuichiro | Whitney, Osceola | Pfenning, Andreas R. | Howard, Jason | Völker, Martin | Skinner, Bejamin M. | Griffin, Darren K. | Ye, Liang | McLaren, William M. | Flicek, Paul | Quesada, Victor | Velasco, Gloria | Lopez-Otin, Carlos | Puente, Xose S. | Olender, Tsviya | Lancet, Doron | Smit, Arian F. A. | Hubley, Robert | Konkel, Miriam K. | Walker, Jerilyn A. | Batzer, Mark A. | Gu, Wanjun | Pollock, David D. | Chen, Lin | Cheng, Ze | Eichler, Evan E. | Stapley, Jessica | Slate, Jon | Ekblom, Robert | Birkhead, Tim | Burke, Terry | Burt, David | Scharff, Constance | Adam, Iris | Richard, Hugues | Sultan, Marc | Soldatov, Alexey | Lehrach, Hans | Edwards, Scott V. | Yang, Shiaw-Pyng | Li, XiaoChing | Graves, Tina | Fulton, Lucinda | Nelson, Joanne | Chinwalla, Asif | Hou, Shunfeng | Mardis, Elaine R. | Wilson, Richard K.
Nature  2010;464(7289):757-762.
The zebra finch is an important model organism in several fields1,2 with unique relevance to human neuroscience3,4. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken5—the only bird with a sequenced genome until now6. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes7. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
doi:10.1038/nature08819
PMCID: PMC3187626  PMID: 20360741
4.  Comparative and demographic analysis of orangutan genomes 
Locke, Devin P. | Hillier, LaDeana W. | Warren, Wesley C. | Worley, Kim C. | Nazareth, Lynne V. | Muzny, Donna M. | Yang, Shiaw-Pyng | Wang, Zhengyuan | Chinwalla, Asif T. | Minx, Pat | Mitreva, Makedonka | Cook, Lisa | Delehaunty, Kim D. | Fronick, Catrina | Schmidt, Heather | Fulton, Lucinda A. | Fulton, Robert S. | Nelson, Joanne O. | Magrini, Vincent | Pohl, Craig | Graves, Tina A. | Markovic, Chris | Cree, Andy | Dinh, Huyen H. | Hume, Jennifer | Kovar, Christie L. | Fowler, Gerald R. | Lunter, Gerton | Meader, Stephen | Heger, Andreas | Ponting, Chris P. | Marques-Bonet, Tomas | Alkan, Can | Chen, Lin | Cheng, Ze | Kidd, Jeffrey M. | Eichler, Evan E. | White, Simon | Searle, Stephen | Vilella, Albert J. | Chen, Yuan | Flicek, Paul | Ma, Jian | Raney, Brian | Suh, Bernard | Burhans, Richard | Herrero, Javier | Haussler, David | Faria, Rui | Fernando, Olga | Darré, Fleur | Farré, Domènec | Gazave, Elodie | Oliva, Meritxell | Navarro, Arcadi | Roberto, Roberta | Capozzi, Oronzo | Archidiacono, Nicoletta | Valle, Giuliano Della | Purgato, Stefania | Rocchi, Mariano | Konkel, Miriam K. | Walker, Jerilyn A. | Ullmer, Brygg | Batzer, Mark A. | Smit, Arian F. A. | Hubley, Robert | Casola, Claudio | Schrider, Daniel R. | Hahn, Matthew W. | Quesada, Victor | Puente, Xose S. | Ordoñez, Gonzalo R. | López-Otín, Carlos | Vinar, Tomas | Brejova, Brona | Ratan, Aakrosh | Harris, Robert S. | Miller, Webb | Kosiol, Carolin | Lawson, Heather A. | Taliwal, Vikas | Martins, André L. | Siepel, Adam | RoyChoudhury, Arindam | Ma, Xin | Degenhardt, Jeremiah | Bustamante, Carlos D. | Gutenkunst, Ryan N. | Mailund, Thomas | Dutheil, Julien Y. | Hobolth, Asger | Schierup, Mikkel H. | Chemnick, Leona | Ryder, Oliver A. | Yoshinaga, Yuko | de Jong, Pieter J. | Weinstock, George M. | Rogers, Jeffrey | Mardis, Elaine R. | Gibbs, Richard A. | Wilson, Richard K.
Nature  2011;469(7331):529-533.
“Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
doi:10.1038/nature09687
PMCID: PMC3060778  PMID: 21270892
5.  The development and characterization of a 60K SNP chip for chicken 
BMC Genomics  2011;12:274.
Background
In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important.
Results
We describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly.
Conclusions
The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.
doi:10.1186/1471-2164-12-274
PMCID: PMC3117858  PMID: 21627800
6.  A vertebrate case study of the quality of assemblies derived from next-generation sequences 
Genome Biology  2011;12(3):R31.
The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.
doi:10.1186/gb-2011-12-3-r31
PMCID: PMC3129681  PMID: 21453517
7.  Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays 
BMC Genomics  2010;11:383.
Background
Tiling arrays have been the tool of choice for probing an organism's transcriptome without prior assumptions about the transcribed regions, but RNA-Seq is becoming a viable alternative as the costs of sequencing continue to decrease. Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs.
Results
Here, we compare these two platforms using a matched sample of poly(A)-enriched RNA isolated from the second larval stage of C. elegans. We find that the raw signals from these two technologies are reasonably well correlated but that RNA-Seq outperforms tiling arrays in several respects, notably in exon boundary detection and dynamic range of expression. By exploring the accuracy of sequencing as a function of depth of coverage, we found that about 4 million reads are required to match the sensitivity of two tiling array replicates. The effects of cross-hybridization were analyzed using a "nearest neighbor" classifier applied to array probes; we describe a method for determining potential "black list" regions whose signals are unreliable. Finally, we propose a strategy for using RNA-Seq data as a gold standard set to calibrate tiling array data. All tiling array and RNA-Seq data sets have been submitted to the modENCODE Data Coordinating Center.
Conclusions
Tiling arrays effectively detect transcript expression levels at a low cost for many species while RNA-Seq provides greater accuracy in several regards. Researchers will need to carefully select the technology appropriate to the biological investigations they are undertaking. It will also be important to reconsider a comparison such as ours as sequencing technologies continue to evolve.
doi:10.1186/1471-2164-11-383
PMCID: PMC3091629  PMID: 20565764
8.  Back to Bermuda: how is science best served? 
Genome Biology  2009;10(4):105.
Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
The independent announcements of two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements and determine the policies for data release and distribution that will best serve both the producers of the data and the users.
doi:10.1186/gb-2009-10-4-105
PMCID: PMC2688919  PMID: 19435531
9.  Genome analysis of the platypus reveals unique signatures of evolution 
Warren, Wesley C. | Hillier, LaDeana W. | Marshall Graves, Jennifer A. | Birney, Ewan | Ponting, Chris P. | Grützner, Frank | Belov, Katherine | Miller, Webb | Clarke, Laura | Chinwalla, Asif T. | Yang, Shiaw-Pyng | Heger, Andreas | Locke, Devin P. | Miethke, Pat | Waters, Paul D. | Veyrunes, Frédéric | Fulton, Lucinda | Fulton, Bob | Graves, Tina | Wallis, John | Puente, Xose S. | López-Otín, Carlos | Ordóñez, Gonzalo R. | Eichler, Evan E. | Chen, Lin | Cheng, Ze | Deakin, Janine E. | Alsop, Amber | Thompson, Katherine | Kirby, Patrick | Papenfuss, Anthony T. | Wakefield, Matthew J. | Olender, Tsviya | Lancet, Doron | Huttley, Gavin A. | Smit, Arian F. A. | Pask, Andrew | Temple-Smith, Peter | Batzer, Mark A. | Walker, Jerilyn A. | Konkel, Miriam K. | Harris, Robert S. | Whittington, Camilla M. | Wong, Emily S. W. | Gemmell, Neil J. | Buschiazzo, Emmanuel | Vargas Jentzsch, Iris M. | Merkel, Angelika | Schmitz, Juergen | Zemann, Anja | Churakov, Gennady | Kriegs, Jan Ole | Brosius, Juergen | Murchison, Elizabeth P. | Sachidanandam, Ravi | Smith, Carly | Hannon, Gregory J. | Tsend-Ayush, Enkhjargal | McMillan, Daniel | Attenborough, Rosalind | Rens, Willem | Ferguson-Smith, Malcolm | Lefèvre, Christophe M. | Sharp, Julie A. | Nicholas, Kevin R. | Ray, David A. | Kube, Michael | Reinhardt, Richard | Pringle, Thomas H. | Taylor, James | Jones, Russell C. | Nixon, Brett | Dacheux, Jean-Louis | Niwa, Hitoshi | Sekita, Yoko | Huang, Xiaoqiu | Stark, Alexander | Kheradpour, Pouya | Kellis, Manolis | Flicek, Paul | Chen, Yuan | Webber, Caleb | Hardison, Ross | Nelson, Joanne | Hallsworth-Pepin, Kym | Delehaunty, Kim | Markovic, Chris | Minx, Pat | Feng, Yucheng | Kremitzki, Colin | Mitreva, Makedonka | Glasscock, Jarret | Wylie, Todd | Wohldmann, Patricia | Thiru, Prathapan | Nhan, Michael N. | Pohl, Craig S. | Smith, Scott M. | Hou, Shunfeng | Renfree, Marilyn B. | Mardis, Elaine R. | Wilson, Richard K.
Nature  2008;453(7192):175-183.
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
doi:10.1038/nature06936
PMCID: PMC2803040  PMID: 18464734
10.  Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse 
PLoS Biology  2009;7(5):e1000112.
A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled duplications contain protein-coding genes that are mostly involved in reproductive function.
The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.
Author Summary
The availability of an accurate genome sequence provides the bedrock upon which modern biomedical research is based. Here we describe a high-quality assembly, Build 36, of the mouse genome. This assembly was put together by aligning overlapping individual clones representing parts of the genome, and it provides a more complete picture than previous assemblies, because it adds much rodent-specific sequence that was previously unavailable. The addition of these sequences provides insight into both the genomic architecture and the gene complement of the mouse. In particular, it highlights recent gene duplications and the expansion of certain gene families during rodent evolution. An improved understanding of the mouse genome and thus mouse biology will enhance the utility of the mouse as a model for human disease.
doi:10.1371/journal.pbio.1000112
PMCID: PMC2680341  PMID: 19468303
11.  Evolutionary Toggling of the MAPT 17q21.31 Inversion Region 
Nature genetics  2008;40(9):1076-1083.
Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and contrast it with the sequence structure and genetic variation of the corresponding 1.5 Mb region for the non-inverted H1 human haplotype and that of chimpanzee and orangutan. We find that inversion of the MAPT region is similarly polymorphic in other great ape species and present evidence that the inversions have occurred independently in both chimpanzee and humans. In humans, the inversion breakpoints correspond to core duplications encoding the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape/human ancestral state with inversion recurrences during primate evolution. We demonstrate that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its preference to undergo microdeletion associated with mental retardation in European populations.
PMCID: PMC2684794  PMID: 19165922
12.  Loss of genes implicated in gastric function during platypus evolution 
Genome Biology  2008;9(5):R81.
Several genes implicated in food digestion have been deleted or inactivated in platypus. This loss perhaps explains the anatomical and physiological differences in the gastrointestinal tract between monotremes and other vertebrates and provides insights into platypus genome evolution.
Background
The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria, which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique opportunity to illuminate some aspects of the biology and evolution of these animals.
Results
We show that several genes implicated in food digestion in the stomach have been deleted or inactivated in platypus. Comparison with other vertebrate genomes revealed that the main genes implicated in the formation and activity of gastric juice have been lost in platypus. These include the aspartyl proteases pepsinogen A and pepsinogens B/C, the hydrochloric acid secretion stimulatory hormone gastrin, and the α subunit of the gastric H+/K+-ATPase. Other genes implicated in gastric functions, such as the β subunit of the H+/K+-ATPase and the aspartyl protease cathepsin E, have been inactivated because of the acquisition of loss-of-function mutations. All of these genes are highly conserved in vertebrates, reflecting a unique pattern of evolution in the platypus genome not previously seen in other mammalian genomes.
Conclusion
The observed loss of genes involved in gastric functions might be responsible for the anatomical and physiological differences in gastrointestinal tract between monotremes and other vertebrates, including small size, lack of glands, and high pH of the monotreme stomach. This study contributes to a better understanding of the mechanisms that underlie the evolution of the platypus genome, might extend the less-is-more evolutionary model to monotremes, and provides novel insights into the importance of gene loss events during mammalian evolution.
doi:10.1186/gb-2008-9-5-r81
PMCID: PMC2441467  PMID: 18482448
13.  Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans 
PLoS Biology  2007;5(11):e310.
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.
Author Summary
Population genomics, the study of genome-wide patterns of sequence variation within and between closely related species, can provide a comprehensive view of the relative importance of mutation, recombination, natural selection, and genetic drift in evolution. It can also provide fundamental insights into the biological attributes of organisms that are specifically shaped by adaptive evolution. One approach for generating population genomic datasets is to align DNA sequences from whole-genome shotgun projects to a standard reference sequence. We used this approach to carry out whole-genome analysis of polymorphism and divergence in Drosophila simulans, a close relative of the model system, D. melanogaster. We find that polymorphism and divergence fluctuate on a large scale across the genome and that these fluctuations are probably explained by natural selection rather than by variation in mutation rates. Our analysis suggests that adaptive protein evolution is common and is often related to biological processes that may be associated with gene expression, chromosome biology, and reproduction. The approaches presented here will have broad applicability to future analysis of population genomic variation in other systems, including humans.
Low-coverage genome sequences from multiple Drosophila simulans strains provide the first comprehensive view of polymorphism and divergence in the fruit fly.
doi:10.1371/journal.pbio.0050310
PMCID: PMC2062478  PMID: 17988176
14.  Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny 
PLoS Biology  2007;5(7):e167.
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 presently.
Author Summary
The importance of chromosomal organization in the fitness of a species is only poorly understood. The publication of the C. elegans genome sequence in 1998 revealed features of higher level organization that suggested its chromosomes were organized into distinct domains. Chromosome arms were accumulating changes more rapidly than the centers of chromosomes. In this paper, we have compared the organization of the nematode C. briggsae genome with that of C. elegans. By building a genetic map based on DNA variations between two strains of C. briggsae, and by using that map to organize the draft genome sequence of C. briggsae published in 2003, we found the following: (1) Intrachromosomal rearrangements are frequent within and even between arms but are less common within central regions and between arms and centers. (2) Genes have remained overwhelmingly on the same chromosomes. (3) The distinctive features that distinguish C. elegans arms from centers also are seen in C. briggsae chromosomes. The conservation of these features between these two species, despite the approximately 100 million years since their most recent common ancestor, provides clear evidence of the selective advantages of the domain architecture of chromosomes. The continuing association of genes on the same chromosomes suggests that this may also be advantageous.
The conservation of both chromosomal organization and synteny between two distantly related species suggests roles for chromosome organization in the fitness of an organism.
doi:10.1371/journal.pbio.0050167
PMCID: PMC1914384  PMID: 17608563
15.  Principles of Genome Evolution in the Drosophila melanogaster Species Group  
PLoS Biology  2007;5(6):e152.
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.
Author Summary
The organization of genes on chromosomes changes over evolutionary time. In some organisms, such as fruit flies and mosquitoes, inversions of chromosome regions are widespread. This has been associated with adaptation to environmental pressures and speciation. However, the mechanisms by which inversions are generated at the molecular level are poorly understood. The prevailing view involves the interactions of sequences that are moderately repeated in the genome. Here, we use molecular and computational methods to study 29 inversions that differentiate the chromosomes of three closely related fruit fly species. We find little support for a causal role of repetitive sequences in the origin of inversions and, instead, detect the presence of inverted duplications of ancestrally unique sequences (generally protein-coding genes) in the breakpoint regions of many inversions. This leads us to propose an alternative model in which the generation of inversions is coupled with the generation of duplications of flanking sequences. Additionally, we find evidence for genomic regions that are prone to breakage, being associated with inversions generated independently during the evolution of the ancestors of existing species.
Chromosomal inversion breakpoints were compared between three closely related Drosophila species. Many are associated with inverted gene duplications, suggesting that the prevalent mechanism for their generation involves staggered breakpoints.
doi:10.1371/journal.pbio.0050152
PMCID: PMC1885836  PMID: 17550304
16.  Application of a superword array in genome assembly 
Nucleic Acids Research  2006;34(1):201-205.
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array. We describe simple algorithms for constructing and using a superword array to find pairs of sequences that share a unique superword. The algorithms are implemented in a genome assembly program called PCAP.REP for computation of overlaps between reads. Experimental results produced by PCAP.REP and PCAP on a whole-genome dataset show that PCAP.REP produced a more accurate and contiguous assembly than PCAP.
doi:10.1093/nar/gkj419
PMCID: PMC1325203  PMID: 16397298
17.  A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans 
PLoS ONE  2011;6(5):e19055.
While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.
doi:10.1371/journal.pone.0019055
PMCID: PMC3094335  PMID: 21602919
18.  Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response 
PLoS Genetics  2010;6(2):e1000848.
Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles.
Author Summary
The C. elegans transcription factor PHA-4 is a member of the highly conserved FOXA family of transcription factors. These factors act as master regulators of organ development by controlling how genes are turned off and on as tissues are formed. Additionally they regulate genes in response to nutrient levels and control both longevity and survival of the organism. However, the extent to which these factors control similar or distinct gene targets for each of these functions is unknown. For this reason, we have used the technique of chromatin immunoprecipitation followed by deep sequencing (ChIP–Seq), to define the target binding sites of PHA-4 on a genome-wide scale, when it is either functioning as an organ identity regulator or in response to environmental stress. Our data clearly demonstrate distinct sets of biologically relevant target genes for the transcription factor PHA-4 under these two different conditions. Not only have we defined PHA-4 targets, but we established an experimental ChIP–Seq pipeline to facilitate the identification of binding sites for many transcription factors in the future.
doi:10.1371/journal.pgen.1000848
PMCID: PMC2824807  PMID: 20174564
19.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome 
Nature  2008;456(7218):66-72.
Lay Summary
Acute myeloid leukemia is a highly malignant hematopoietic tumor that affects about 13,000 adults yearly in the United States. The treatment of this disease has changed little in the past two decades, since most of the genetic events that initiate the disease remain undiscovered. Whole genome sequencing is now possible at a reasonable cost and timeframe to utilize this approach for unbiased discovery of tumor-specific somatic mutations that alter the protein-coding genes. Here we show the results obtained by sequencing a typical acute myeloid leukemia genome and its matched normal counterpart, obtained from the patient’s skin. We discovered 10 genes with acquired mutations; two were previously described mutations thought to contribute to tumor progression, and 8 were novel mutations present in virtually all tumor cells at presentation and relapse, whose function is not yet known. Our study establishes whole genome sequencing as an unbiased method for discovering initiating mutations in cancer genomes, and for identifying novel genes that may respond to targeted therapies.
We used massively parallel sequencing technology to sequence the genomic DNA of tumor and normal skin cells obtained from a patient with a typical presentation of FAB M1 Acute Myeloid Leukemia (AML) with normal cytogenetics. 32.7-fold ‘haploid’ coverage (98 billion bases) was obtained for the tumor genome, and 13.9-fold coverage (41.8 billion bases) was obtained for the normal sample. Of 2,647,695 well-supported Single Nucleotide Variants (SNVs) found in the tumor genome, 2,588,486 (97.7%) also were detected in the patient’s skin genome, limiting the number of variants that required further study. For the purposes of this initial study, we restricted our downstream analysis to the coding sequences of annotated genes: we found only eight heterozygous, non-synonymous somatic SNVs in the entire genome. All were novel, including mutations in protocadherin/cadherin family members (CDH24 and PCLKC), G-protein coupled receptors (GPR123 and EBI2), a protein phosphatase (PTPRT), a potential guanine nucleotide exchange factor (KNDC1), a peptide/drug transporter (SLC15A1), and a glutamate receptor gene (GRINL1B). We also detected previously described, recurrent somatic insertions in the FLT3 and NPM1 genes. Based on deep readcount data, we determined that all of these mutations (except FLT3) were present in nearly all tumor cells at presentation, and again at relapse 11 months later, suggesting that the patient had a single dominant clone containing all of the mutations. These results demonstrate the power of whole genome sequencing to discover novel cancer-associated mutations.
doi:10.1038/nature07485
PMCID: PMC2603574  PMID: 18987736
20.  Design and implementation of a generalized laboratory data model 
BMC Bioinformatics  2007;8:362.
Background
Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable.
Results
We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.
Conclusion
The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.
doi:10.1186/1471-2105-8-362
PMCID: PMC2194795  PMID: 17897463
21.  The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics 
PLoS Biology  2003;1(2):e45.
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.
With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome evolution
doi:10.1371/journal.pbio.0000045
PMCID: PMC261899  PMID: 14624247

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