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Article ; Online: Rapid and sensitive detection of genome contamination at scale with FCS-GX.

Astashyn, Alexander / Tvedte, Eric S / Sweeney, Deacon / Sapojnikov, Victor / Bouk, Nathan / Joukov, Victor / Mozes, Eyal / Strope, Pooja K / Sylla, Pape M / Wagner, Lukas / Bidwell, Shelby L / Brown, Larissa C / Clark, Karen / Davis, Emily W / Smith-White, Brian / Hlavina, Wratko / Pruitt, Kim D / Schneider, Valerie A / Murphy, Terence D

Genome biology

2024 Volume 25, Issue 1, Page(s) 60

Abstract: Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most ... ...

Abstract	Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 min. Testing FCS-GX on artificially fragmented genomes demonstrates high sensitivity and specificity for diverse contaminant species. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination, comprising 0.16% of total bases, with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/ or https://doi.org/10.5281/zenodo.10651084 .
MeSH term(s)	Genome ; Databases, Nucleic Acid ; Software
Language	English
Publishing date	2024-02-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-024-03198-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Rapid and sensitive detection of genome contamination at scale with FCS-GX.

Astashyn, Alexander / Tvedte, Eric S / Sweeney, Deacon / Sapojnikov, Victor / Bouk, Nathan / Joukov, Victor / Mozes, Eyal / Strope, Pooja K / Sylla, Pape M / Wagner, Lukas / Bidwell, Shelby L / Clark, Karen / Davis, Emily W / Smith-White, Brian / Hlavina, Wratko / Pruitt, Kim D / Schneider, Valerie A / Murphy, Terence D

bioRxiv : the preprint server for biology

2023

Abstract	Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (0.16% of total bases), with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/.
Language	English
Publishing date	2023-06-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.02.543519
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

O'Leary, Nuala A / Wright, Mathew W / Brister, J Rodney / Ciufo, Stacy / Haddad, Diana / McVeigh, Rich / Rajput, Bhanu / Robbertse, Barbara / Smith-White, Brian / Ako-Adjei, Danso / Astashyn, Alexander / Badretdin, Azat / Bao, Yiming / Blinkova, Olga / Brover, Vyacheslav / Chetvernin, Vyacheslav / Choi, Jinna / Cox, Eric / Ermolaeva, Olga /

Farrell, Catherine M / Goldfarb, Tamara / Gupta, Tripti / Haft, Daniel / Hatcher, Eneida / Hlavina, Wratko / Joardar, Vinita S / Kodali, Vamsi K / Li, Wenjun / Maglott, Donna / Masterson, Patrick / McGarvey, Kelly M / Murphy, Michael R / O'Neill, Kathleen / Pujar, Shashikant / Rangwala, Sanjida H / Rausch, Daniel / Riddick, Lillian D / Schoch, Conrad / Shkeda, Andrei / Storz, Susan S / Sun, Hanzhen / Thibaud-Nissen, Francoise / Tolstoy, Igor / Tully, Raymond E / Vatsan, Anjana R / Wallin, Craig / Webb, David / Wu, Wendy / Landrum, Melissa J / Kimchi, Avi / Tatusova, Tatiana / DiCuccio, Michael / Kitts, Paul / Murphy, Terence D / Pruitt, Kim D

Nucleic acids research

2016 Volume 44, Issue D1, Page(s) D733–45

Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project ... ...

Abstract	The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
MeSH term(s)	Animals ; Cattle ; Databases, Genetic ; Gene Expression Profiling ; Genome, Fungal ; Genome, Human ; Genome, Microbial ; Genome, Plant ; Genome, Viral ; Genomics/standards ; Humans ; Invertebrates/genetics ; Mice ; Molecular Sequence Annotation ; Nematoda/genetics ; Phylogeny ; RNA, Long Noncoding/genetics ; Rats ; Reference Standards ; Sequence Analysis, Protein ; Sequence Analysis, RNA ; Vertebrates/genetics
Chemical Substances	RNA, Long Noncoding
Keywords	covid19
Language	English
Publishing date	2016-01-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv1189
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Lineage-specific biology revealed by a finished genome assembly of the mouse.

Church, Deanna M / Goodstadt, Leo / Hillier, Ladeana W / Zody, Michael C / Goldstein, Steve / She, Xinwe / Bult, Carol J / Agarwala, Richa / Cherry, Joshua L / DiCuccio, Michael / Hlavina, Wratko / Kapustin, Yuri / Meric, Peter / Maglott, Donna / Birtle, Zoë / Marques, Ana C / Graves, Tina / Zhou, Shiguo / Teague, Brian /

Potamousis, Konstantinos / Churas, Christopher / Place, Michael / Herschleb, Jill / Runnheim, Ron / Forrest, Daniel / Amos-Landgraf, James / Schwartz, David C / Cheng, Ze / Lindblad-Toh, Kerstin / Eichler, Evan E / Ponting, Chris P

PLoS biology

2009 Volume 7, Issue 5, Page(s) e1000112

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Animals ; Computational Biology/methods ; Databases, Genetic ; Gene Duplication ; Genome/genetics ; Genome/physiology ; Humans ; Mice
Language	English
Publishing date	2009-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.1000112
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The genome of the sea urchin Strongylocentrotus purpuratus.

Sodergren, Erica / Weinstock, George M / Davidson, Eric H / Cameron, R Andrew / Gibbs, Richard A / Angerer, Robert C / Angerer, Lynne M / Arnone, Maria Ina / Burgess, David R / Burke, Robert D / Coffman, James A / Dean, Michael / Elphick, Maurice R / Ettensohn, Charles A / Foltz, Kathy R / Hamdoun, Amro / Hynes, Richard O / Klein, William H / Marzluff, William /

McClay, David R / Morris, Robert L / Mushegian, Arcady / Rast, Jonathan P / Smith, L Courtney / Thorndyke, Michael C / Vacquier, Victor D / Wessel, Gary M / Wray, Greg / Zhang, Lan / Elsik, Christine G / Ermolaeva, Olga / Hlavina, Wratko / Hofmann, Gretchen / Kitts, Paul / Landrum, Melissa J / Mackey, Aaron J / Maglott, Donna / Panopoulou, Georgia / Poustka, Albert J / Pruitt, Kim / Sapojnikov, Victor / Song, Xingzhi / Souvorov, Alexandre / Solovyev, Victor / Wei, Zheng / Whittaker, Charles A / Worley, Kim / Durbin, K James / Shen, Yufeng / Fedrigo, Olivier / Garfield, David / Haygood, Ralph / Primus, Alexander / Satija, Rahul / Severson, Tonya / Gonzalez-Garay, Manuel L / Jackson, Andrew R / Milosavljevic, Aleksandar / Tong, Mark / Killian, Christopher E / Livingston, Brian T / Wilt, Fred H / Adams, Nikki / Bellé, Robert / Carbonneau, Seth / Cheung, Rocky / Cormier, Patrick / Cosson, Bertrand / Croce, Jenifer / Fernandez-Guerra, Antonio / Genevière, Anne-Marie / Goel, Manisha / Kelkar, Hemant / Morales, Julia / Mulner-Lorillon, Odile / Robertson, Anthony J / Goldstone, Jared V / Cole, Bryan / Epel, David / Gold, Bert / Hahn, Mark E / Howard-Ashby, Meredith / Scally, Mark / Stegeman, John J / Allgood, Erin L / Cool, Jonah / Judkins, Kyle M / McCafferty, Shawn S / Musante, Ashlan M / Obar, Robert A / Rawson, Amanda P / Rossetti, Blair J / Gibbons, Ian R / Hoffman, Matthew P / Leone, Andrew / Istrail, Sorin / Materna, Stefan C / Samanta, Manoj P / Stolc, Viktor / Tongprasit, Waraporn / Tu, Qiang / Bergeron, Karl-Frederik / Brandhorst, Bruce P / Whittle, James / Berney, Kevin / Bottjer, David J / Calestani, Cristina / Peterson, Kevin / Chow, Elly / Yuan, Qiu Autumn / Elhaik, Eran / Graur, Dan / Reese, Justin T / Bosdet, Ian / Heesun, Shin / Marra, Marco A / Schein, Jacqueline / Anderson, Michele K / Brockton, Virginia / Buckley, Katherine M / Cohen, Avis H / Fugmann, Sebastian D / Hibino, Taku / Loza-Coll, Mariano / Majeske, Audrey J / Messier, Cynthia / Nair, Sham V / Pancer, Zeev / Terwilliger, David P / Agca, Cavit / Arboleda, Enrique / Chen, Nansheng / Churcher, Allison M / Hallböök, F / Humphrey, Glen W / Idris, Mohammed M / Kiyama, Takae / Liang, Shuguang / Mellott, Dan / Mu, Xiuqian / Murray, Greg / Olinski, Robert P / Raible, Florian / Rowe, Matthew / Taylor, John S / Tessmar-Raible, Kristin / Wang, D / Wilson, Karen H / Yaguchi, Shunsuke / Gaasterland, Terry / Galindo, Blanca E / Gunaratne, Herath J / Juliano, Celina / Kinukawa, Masashi / Moy, Gary W / Neill, Anna T / Nomura, Mamoru / Raisch, Michael / Reade, Anna / Roux, Michelle M / Song, Jia L / Su, Yi-Hsien / Townley, Ian K / Voronina, Ekaterina / Wong, Julian L / Amore, Gabriele / Branno, Margherita / Brown, Euan R / Cavalieri, Vincenzo / Duboc, Véronique / Duloquin, Louise / Flytzanis, Constantin / Gache, Christian / Lapraz, François / Lepage, Thierry / Locascio, Annamaria / Martinez, Pedro / Matassi, Giorgio / Matranga, Valeria / Range, Ryan / Rizzo, Francesca / Röttinger, Eric / Beane, Wendy / Bradham, Cynthia / Byrum, Christine / Glenn, Tom / Hussain, Sofia / Manning, Gerard / Miranda, Esther / Thomason, Rebecca / Walton, Katherine / Wikramanayke, Athula / Wu, Shu-Yu / Xu, Ronghui / Brown, C Titus / Chen, Lili / Gray, Rachel F / Lee, Pei Yun / Nam, Jongmin / Oliveri, Paola / Smith, Joel / Muzny, Donna / Bell, Stephanie / Chacko, Joseph / Cree, Andrew / Curry, Stacey / Davis, Clay / Dinh, Huyen / Dugan-Rocha, Shannon / Fowler, Jerry / Gill, Rachel / Hamilton, Cerrissa / Hernandez, Judith / Hines, Sandra / Hume, Jennifer / Jackson, Laronda / Jolivet, Angela / Kovar, Christie / Lee, Sandra / Lewis, Lora / Miner, George / Morgan, Margaret / Nazareth, Lynne V / Okwuonu, Geoffrey / Parker, David / Pu, Ling-Ling / Thorn, Rachel / Wright, Rita

Science (New York, N.Y.)

2007 Volume 314, Issue 5801, Page(s) 941–952

Abstract: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) ...

Abstract	We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
MeSH term(s)	Animals ; Calcification, Physiologic ; Cell Adhesion Molecules/genetics ; Cell Adhesion Molecules/physiology ; Complement Activation/genetics ; Computational Biology ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes ; Genome ; Immunity, Innate/genetics ; Immunologic Factors/genetics ; Immunologic Factors/physiology ; Male ; Nervous System Physiological Phenomena ; Proteins/genetics ; Proteins/physiology ; Sequence Analysis, DNA ; Signal Transduction ; Strongylocentrotus purpuratus/embryology ; Strongylocentrotus purpuratus/genetics ; Strongylocentrotus purpuratus/immunology ; Strongylocentrotus purpuratus/physiology ; Transcription Factors/genetics
Chemical Substances	Cell Adhesion Molecules ; Immunologic Factors ; Proteins ; Transcription Factors
Language	English
Publishing date	2007-03-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1133609
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Genome of the Sea Urchin Strongylocentrotus purpuratus

Sodergren, Erica / Adams, Nikki / Agca, Cavit / Allgood, Erin L / Amore, Gabriele / Anderson, Michele K / Angerer, Lynne M / Angerer, Robert C / Arboleda, Enrique / Arnone, Maria Ina / Beane, Wendy / Bell, Stephanie / BellÃ©, Robert / Bergeron, Karl-Frederik / Berney, Kevin / Bosdet, Ian / Bottjer, David J / Bradham, Cynthia / Brandhorst, Bruce P /

Branno, Margherita / Brockton, Virginia / Brown, C. Titus / Brown, Euan R / Buckley, Katherine M / Burgess, David R / Burke, Robert D / Byrum, Christine / Calestani, Cristina / Cameron, R. Andrew / Carbonneau, Seth / Cavalieri, Vincenzo / Chacko, Joseph / Chen, Lili / Chen, Nansheng / Cheung, Rocky / Chow, Elly / Churcher, Allison M / Coffman, James A / Cohen, Avis H / Cole, Bryan / Cool, Jonah / Cormier, Patrick / Cosson, Bertrand / Cree, Andrew / Croce, Jenifer / Curry, Stacey / Davidson, Eric H / Davis, Clay / Dean, Michael / Dinh, Huyen / Duboc, VÃ©ronique / Dugan-Rocha, Shannon / Duloquin, Louise / Durbin, K. James / Elhaik, Eran / Elphick, Maurice R / Elsik, Christine G / Epel, David / Ermolaeva, Olga / Ettensohn, Charles A / Fedrigo, Olivier / Fernandez-Guerra, Antonio / Flytzanis, Constantin / Foltz, Kathy R / Fowler, Jerry / Fugmann, Sebastian D / Gaasterland, Terry / Gache, Christian / Galindo, Blanca E / Garfield, David / GeneviÃ¨re, Anne-Marie / Gibbons, Ian R / Gibbs, Richard A / Gill, Rachel / Glenn, Tom / Goel, Manisha / Gold, Bert / Goldstone, Jared V / Gonzalez-Garay, Manuel L / Graur, Dan / Gray, Rachel F / Gunaratne, Herath J / Hahn, Mark E / HallbÃ¶Ã¶k, F / Hamdoun, Amro / Hamilton, Cerrissa / Haygood, Ralph / Heesun, Shin / Hernandez, Judith / Hibino, Taku / Hines, Sandra / Hlavina, Wratko / Hoffman, Matthew P / Hofmann, Gretchen / Howard-Ashby, Meredith / Hume, Jennifer / Humphrey, Glen W / Hussain, Sofia / Hynes, Richard O / Idris, Mohammed M / Istrail, Sorin / Jackson, Andrew R / Jackson, LaRonda / Jolivet, Angela / Judkins, Kyle M / Juliano, Celina / Kelkar, Hemant / Killian, Christopher E / Kinukawa, Masashi / Kitts, Paul / Kiyama, Takae / Klein, William H / Kovar, Christie / Landrum, Melissa J / Lapraz, FranÃ§ois / Lee, Pei Yun / Lee, Sandra / Leone, Andrew / Lepage, Thierry / Lewis, Lora / Liang, Shuguang / Livingston, Brian T / Locascio, Annamaria / Loza-Coll, Mariano / Mackey, Aaron J / Maglott, Donna / Majeske, Audrey J / Manning, FranÃ§ois Gerard / Marra, Marco A / Martinez, Pedro / Marzluff, William / Matassi, Giorgio / Materna, Stefan C / Matranga, Valeria / McCafferty, Shawn S / McClay, David R / Mellott, Dan / Messier, Cynthia / Milosavljevic, Aleksandar / Miner, George / Miranda, Esther / Morales, Julia / Morgan, Margaret / Morris, Robert L / Moy, Gary W / Mu, Xiuqian / Mulner-Lorillon, Odile / Murray, Greg / Musante, Ashlan M / Mushegian, Arcady / Muzny, Donna / Nair, Sham V / Nam, Jongmin / Nazareth, Lynne V / Neill, Anna T / Nomura, Mamoru / Obar, Robert A / Okwuonu, Geoffrey / Olinski, Robert P / Oliveri, Paola / Pancer, Zeev / Panopoulou, Georgia / Parker, David / Peterson, Kevin / Poustka, Albert J / Primus, Alexander / Pruitt, Kim / Pu, Ling-Ling / RÃ¶ttinger, Eric / Raible, Florian / Raisch, Michael / Range, Ryan / Rast, Jonathan P / Rawson, Amanda P / Reade, Anna / Reese, Justin T / Rizzo, Francesca / Robertson, Anthony J / Rossetti, Blair J / Roux, Michelle M / Rowe, Matthew / Samanta, Manoj P / Sapojnikov, Victor / Satija, Rahul / Scally, Mark / Schein, Jacqueline / Severson, Tonya / Shen, Yufeng / Smith, Joel / Smith, L. Courtney / Solovyev, Victor / Song, Jia L / Song, Xingzhi / Souvorov, Alexandre / Stegeman, John J / Stolc, Viktor / Su, Yi-Hsien / Taylor, John S / Terwilliger, David P / Tessmar-Raible, Kristin / Thomason, Rebecca / Thorn, Rachel / Thorndyke, Michael C / Tong, Mark / Tongprasit, Waraporn / Townley, Ian K / Tu, Qiang / Vacquier, Victor D / Voronina, Ekaterina / Walton, Katherine / Wang, D / Wei, Zheng / Weinstock, George M / Wessel, Gary M / Whittaker, Charles A / Whittle, James / Wikramanayke, Athula / Wilson, Karen H / Wilt, Fred H / Wong, Julian L / Worley, Kim / Wray, Greg / Wright, Rita / Wu, Shu-Yu / Xu, Ronghui / Yaguchi, Shunsuke / Yuan, Qiu Autumn / Zhang, Lan

Science. 2006 Nov. 10, v. 314, no. 5801

2006

Abstract	We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
Keywords	bacterial artificial chromosomes ; Chordata ; clones ; evolution ; genes ; heterozygosity ; models ; sequence analysis ; Strongylocentrotus purpuratus ; vertebrates
Language	English
Dates of publication	2006-1110
Size	p. 941-952.
Publishing place	American Association for the Advancement of Science
Document type	Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1133609
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genome sequence of the pea aphid Acyrthosiphon pisum

Richards, Stephen / Gibbs, Richard A. / Gerardo, Nicole M. / Moran, Nancy / Nakabachi, Atsushi / Stern, David / Tagu, Denis / Wilson, Alex C.C. / Muzny, Donna / Kovar, Christie / Cree, Andy / Chacko, Joseph / Chandrabose, Mimi N. / Dao, Marvin Diep / Dinh, Huyen H. / Gabisi, Ramatu Ayiesha / Hines, Sandra / Hume, Jennifer / Jhangian, Shalini N. /

Joshi, Vandita / Lewis, Lora R. / Liu, Yih Shin / Lopez, John / Morgan, Margaret B. / Nguyen, Ngoc Bich / Okwuonu, Geoffrey O. / Ruiz, San Juana / Santibanez, Jireh / Wright, Rita A. / Fowler, Gerald R. / Hitchens, Matthew E. / Lozado, Ryan J. / Moen, Charles / Steffen, David / Warren, James T. / Zhang, Jingkun / Nazareth, Lynne V. / Chavez, Dean / Davis, Clay / Lee, Sandra L. / Patel, Bella Mayurkumar / Pu, Ling Ling / Bell, Stephanie N. / Johnson, Angela Jolivet / Vattathil, Selina / Williams, Rex L. / Shigenobu, Shuji / Dang, Phat M. / Morioka, Mizue / Fukatsu, Takema / Kudo, Toshiaki / Miyagishima, Shin Ya / Jiang, Huaiyang / Worley, Kim C. / Legeai, Fabrice / Gauthier, Jean Pierre / Collin, Olivier / Zhang, Lan / Chen, Hsiu Chuan / Ermolaeva, Olga / Hlavina, Wratko / Kapustin, Yuri / Kiryutin, Boris / Kitts, Paul / Maglott, Donna / Murphy, Terence / Pruitt, Kim / Sapojnikov, Victor / Souvorov, Alexandre / Thibaud-Nissen, Françoise / Câmara, Francisco / Guigó, Roderic / Stanke, Mario / Solovyev, Victor / Kosarev, Peter / Gilbert, Don / Gabaldón, Toni / Huerta-Cepas, Jaime / Marcet-Houben, Marina / Pignatelli, Miguel / Moya, Andrés / Rispe, Claude / Ollivier, Morgane / Quesneville, Hadi / Permal, Emmanuelle / Llorens, Carlos / Futami, Ricardo / Hedges, Dale / Robertson, Hugh M. / Alioto, Tyler / Mariotti, Marco / Nikoh, Naruo / McCutcheon, John P. / Burke, Gaelen / Kamins, Alexandra / Latorre, Amparo / Ashton, Peter / Calevro, Federica / Charles, Hubert / Colella, Stefano / Douglas, Angela E. / Jander, Georg / Jones, Derek H. / Febvay, Gérard / Kamphuis, Lars G. / Kushlan, Philip F. / Macdonald, Sandy / Ramsey, John / Schwartz, Julia / Seah, Stuart / Thomas, Gavin / Vellozo, Augusto / Cass, Bodil / Degnan, Patrick / Hurwitz, Bonnie / Leonardo, Teresa / Koga, Ryuichi / Altincicek, Boran / Anselme, Caroline / Atamian, Hagop / Barribeau, Seth M. / De Vos, Martin / Duncan, Elizabeth / Evans, Jay / Ghanim, Murad / Heddi, Abdelaziz / Kaloshian, Isgouhi / Vincent-Monegat, Carole / Parker, Ben J. / Pérez-Brocal, Vicente / Rahbé, Yvan / Spragg, Chelsea J. / Tamames, Javier / Tamarit, Daniel / Tamborindeguy, Cecilia / Vilcinskas, Andreas / Bickel, Ryan D. / Brisson, Jennifer A. / Butts, Thomas / Chang, Chun Che / Christiaens, Olivier / Davis, Gregory K. / Ferrier, David / Iga, Masatoshi / Janssen, Ralf / Lu, Hsiao Ling / McGregor, Alistair / Miura, Toru / Smagghe, Guy / Smith, James / Van Der Zee, Maurijn / Velarde, Rodrigo / Wilson, Megan / Dearden, Peter / Edwards, Owain R. / Gordon, Karl / Hilgarth, Roland S. / Rider, Stanley Dean / Srinivasan, Dayalan / Walsh, Thomas K. / Ishikawa, Asano / Jaubert-Possamai, Stéphanie / Fenton, Brian / Huang, Wenting / Rizk, Guillaume / Lavenier, Dominique / Nicolas, Jacques / Smadja, Carole / Zhou, Jing Jiang / Vieira, Filipe G. / He, Xiao Li / Liu, Renhu / Rozas, Julio / Field, Linda M. / Campbell, Peter / Carolan, James C. / Fitzroy, Carol I.J. / Reardon, Karen T. / Reeck, Gerald R. / Singh, Karam / Wilkinson, Thomas L. / Huybrechts, Jurgen / Abdel-Latief, Mohatmed / Robichon, Alain / Veenstra, Jan A. / Hauser, Frank / Cazzamali, Giuseppe / Schneider, Martina / Williamson, Michael / Stafflinger, Elisabeth / Hansen, Karina K. / Grimmelikhuijzen, Cornelis J.P. / Price, Daniel R.G. / Caillaud, Marina / Van Fleet, Eric / Ren, Qinghu / Gatehouse, John A. / Brault, Véronique / Monsion, Baptiste / Diaz, Jason / Hunnicutt, Laura / Ju, Ho Jong / Pechuan, Ximo / Aguilar, José / Cortés, Teresa / Ortiz-Rivas, Benjamín / Martínez-Torres, David / Dombrovsky, Aviv / Dale, Richard P. / Davies, T.G.E. / Williamson, Martin S. / Jones, Andrew / Sattelle, David / Williamson, Sally / Wolstenholme, Adrian / Cottret, Ludovic / Sagot, Marie France / Heckel, David G. / Hunter, Wayne

PloS Biology

2010 Volume 8, Issue 2

Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of ... ...

Abstract	Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Keywords	Life Science
Subject code	612
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The genome of the model beetle and pest Tribolium castaneum.

Richards, Stephen / Gibbs, Richard A / Weinstock, George M / Brown, Susan J / Denell, Robin / Beeman, Richard W / Gibbs, Richard / Bucher, Gregor / Friedrich, Markus / Grimmelikhuijzen, Cornelis J P / Klingler, Martin / Lorenzen, Marce / Roth, Siegfried / Schröder, Reinhard / Tautz, Diethard / Zdobnov, Evgeny M / Muzny, Donna / Attaway, Tony / Bell, Stephanie /

Buhay, Christian J / Chandrabose, Mimi N / Chavez, Dean / Clerk-Blankenburg, Kerstin P / Cree, Andrew / Dao, Marvin / Davis, Clay / Chacko, Joseph / Dinh, Huyen / Dugan-Rocha, Shannon / Fowler, Gerald / Garner, Toni T / Garnes, Jeffrey / Gnirke, Andreas / Hawes, Alica / Hernandez, Judith / Hines, Sandra / Holder, Michael / Hume, Jennifer / Jhangiani, Shalini N / Joshi, Vandita / Khan, Ziad Mohid / Jackson, LaRonda / Kovar, Christie / Kowis, Andrea / Lee, Sandra / Lewis, Lora R / Margolis, Jon / Morgan, Margaret / Nazareth, Lynne V / Nguyen, Ngoc / Okwuonu, Geoffrey / Parker, David / Ruiz, San-Juana / Santibanez, Jireh / Savard, Joël / Scherer, Steven E / Schneider, Brian / Sodergren, Erica / Vattahil, Selina / Villasana, Donna / White, Courtney S / Wright, Rita / Park, Yoonseong / Lord, Jeff / Oppert, Brenda / Brown, Susan / Wang, Liangjiang / Weinstock, George / Liu, Yue / Worley, Kim / Elsik, Christine G / Reese, Justin T / Elhaik, Eran / Landan, Giddy / Graur, Dan / Arensburger, Peter / Atkinson, Peter / Beidler, Jim / Demuth, Jeffery P / Drury, Douglas W / Du, Yu-Zhou / Fujiwara, Haruhiko / Maselli, Vincenza / Osanai, Mizuko / Robertson, Hugh M / Tu, Zhijian / Wang, Jian-jun / Wang, Suzhi / Song, Henry / Zhang, Lan / Werner, Doreen / Stanke, Mario / Morgenstern, Burkhard / Solovyev, Victor / Kosarev, Peter / Brown, Garth / Chen, Hsiu-Chuan / Ermolaeva, Olga / Hlavina, Wratko / Kapustin, Yuri / Kiryutin, Boris / Kitts, Paul / Maglott, Donna / Pruitt, Kim / Sapojnikov, Victor / Souvorov, Alexandre / Mackey, Aaron J / Waterhouse, Robert M / Wyder, Stefan / Kriventseva, Evgenia V / Kadowaki, Tatsuhiko / Bork, Peer / Aranda, Manuel / Bao, Riyue / Beermann, Anke / Berns, Nicola / Bolognesi, Renata / Bonneton, François / Bopp, Daniel / Butts, Thomas / Chaumot, Arnaud / Denell, Robin E / Ferrier, David E K / Gordon, Cassondra M / Jindra, Marek / Lan, Que / Lattorff, H Michael G / Laudet, Vincent / von Levetsow, Cornelia / Liu, Zhenyi / Lutz, Rebekka / Lynch, Jeremy A / da Fonseca, Rodrigo Nunes / Posnien, Nico / Reuter, Rolf / Schinko, Johannes B / Schmitt, Christian / Schoppmeier, Michael / Shippy, Teresa D / Simonnet, Franck / Marques-Souza, Henrique / Tomoyasu, Yoshinori / Trauner, Jochen / Van der Zee, Maurijn / Vervoort, Michel / Wittkopp, Nadine / Wimmer, Ernst A / Yang, Xiaoyun / Jones, Andrew K / Sattelle, David B / Ebert, Paul R / Nelson, David / Scott, Jeffrey G / Muthukrishnan, Subbaratnam / Kramer, Karl J / Arakane, Yasuyuki / Zhu, Qingsong / Hogenkamp, David / Dixit, Radhika / Jiang, Haobo / Zou, Zhen / Marshall, Jeremy / Elpidina, Elena / Vinokurov, Konstantin / Oppert, Cris / Evans, Jay / Lu, Zhiqiang / Zhao, Picheng / Sumathipala, Niranji / Altincicek, Boran / Vilcinskas, Andreas / Williams, Michael / Hultmark, Dan / Hetru, Charles / Hauser, Frank / Cazzamali, Giuseppe / Williamson, Michael / Li, Bin / Tanaka, Yoshiaki / Predel, Reinhard / Neupert, Susanne / Schachtner, Joachim / Verleyen, Peter / Raible, Florian / Walden, Kimberly K O / Angeli, Sergio / Forêt, Sylvain / Schuetz, Stefan / Maleszka, Ryszard / Miller, Sherry C / Grossmann, Daniela

Nature

2008 Volume 452, Issue 7190, Page(s) 949–955

Abstract: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This ... ...

Abstract	Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
MeSH term(s)	Animals ; Base Composition ; Body Patterning/genetics ; Cytochrome P-450 Enzyme System/genetics ; DNA Transposable Elements/genetics ; Genes, Insect/genetics ; Genome, Insect/genetics ; Growth and Development/genetics ; Humans ; Insecticides/pharmacology ; Neurotransmitter Agents/genetics ; Oogenesis/genetics ; Phylogeny ; Proteome/genetics ; RNA Interference ; Receptors, G-Protein-Coupled/genetics ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Taste/genetics ; Telomere/genetics ; Tribolium/classification ; Tribolium/embryology ; Tribolium/genetics ; Tribolium/physiology ; Vision, Ocular/genetics
Chemical Substances	DNA Transposable Elements ; Insecticides ; Neurotransmitter Agents ; Proteome ; Receptors, G-Protein-Coupled ; Receptors, Odorant ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2008-03-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature06784
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Initial sequencing and comparative analysis of the mouse genome.

Waterston, Robert H / Lindblad-Toh, Kerstin / Birney, Ewan / Rogers, Jane / Abril, Josep F / Agarwal, Pankaj / Agarwala, Richa / Ainscough, Rachel / Alexandersson, Marina / An, Peter / Antonarakis, Stylianos E / Attwood, John / Baertsch, Robert / Bailey, Jonathon / Barlow, Karen / Beck, Stephan / Berry, Eric / Birren, Bruce / Bloom, Toby /

Bork, Peer / Botcherby, Marc / Bray, Nicolas / Brent, Michael R / Brown, Daniel G / Brown, Stephen D / Bult, Carol / Burton, John / Butler, Jonathan / Campbell, Robert D / Carninci, Piero / Cawley, Simon / Chiaromonte, Francesca / Chinwalla, Asif T / Church, Deanna M / Clamp, Michele / Clee, Christopher / Collins, Francis S / Cook, Lisa L / Copley, Richard R / Coulson, Alan / Couronne, Olivier / Cuff, James / Curwen, Val / Cutts, Tim / Daly, Mark / David, Robert / Davies, Joy / Delehaunty, Kimberly D / Deri, Justin / Dermitzakis, Emmanouil T / Dewey, Colin / Dickens, Nicholas J / Diekhans, Mark / Dodge, Sheila / Dubchak, Inna / Dunn, Diane M / Eddy, Sean R / Elnitski, Laura / Emes, Richard D / Eswara, Pallavi / Eyras, Eduardo / Felsenfeld, Adam / Fewell, Ginger A / Flicek, Paul / Foley, Karen / Frankel, Wayne N / Fulton, Lucinda A / Fulton, Robert S / Furey, Terrence S / Gage, Diane / Gibbs, Richard A / Glusman, Gustavo / Gnerre, Sante / Goldman, Nick / Goodstadt, Leo / Grafham, Darren / Graves, Tina A / Green, Eric D / Gregory, Simon / Guigó, Roderic / Guyer, Mark / Hardison, Ross C / Haussler, David / Hayashizaki, Yoshihide / Hillier, LaDeana W / Hinrichs, Angela / Hlavina, Wratko / Holzer, Timothy / Hsu, Fan / Hua, Axin / Hubbard, Tim / Hunt, Adrienne / Jackson, Ian / Jaffe, David B / Johnson, L Steven / Jones, Matthew / Jones, Thomas A / Joy, Ann / Kamal, Michael / Karlsson, Elinor K / Karolchik, Donna / Kasprzyk, Arkadiusz / Kawai, Jun / Keibler, Evan / Kells, Cristyn / Kent, W James / Kirby, Andrew / Kolbe, Diana L / Korf, Ian / Kucherlapati, Raju S / Kulbokas, Edward J / Kulp, David / Landers, Tom / Leger, J P / Leonard, Steven / Letunic, Ivica / Levine, Rosie / Li, Jia / Li, Ming / Lloyd, Christine / Lucas, Susan / Ma, Bin / Maglott, Donna R / Mardis, Elaine R / Matthews, Lucy / Mauceli, Evan / Mayer, John H / McCarthy, Megan / McCombie, W Richard / McLaren, Stuart / McLay, Kirsten / McPherson, John D / Meldrim, Jim / Meredith, Beverley / Mesirov, Jill P / Miller, Webb / Miner, Tracie L / Mongin, Emmanuel / Montgomery, Kate T / Morgan, Michael / Mott, Richard / Mullikin, James C / Muzny, Donna M / Nash, William E / Nelson, Joanne O / Nhan, Michael N / Nicol, Robert / Ning, Zemin / Nusbaum, Chad / O'Connor, Michael J / Okazaki, Yasushi / Oliver, Karen / Overton-Larty, Emma / Pachter, Lior / Parra, Genís / Pepin, Kymberlie H / Peterson, Jane / Pevzner, Pavel / Plumb, Robert / Pohl, Craig S / Poliakov, Alex / Ponce, Tracy C / Ponting, Chris P / Potter, Simon / Quail, Michael / Reymond, Alexandre / Roe, Bruce A / Roskin, Krishna M / Rubin, Edward M / Rust, Alistair G / Santos, Ralph / Sapojnikov, Victor / Schultz, Brian / Schultz, Jörg / Schwartz, Matthias S / Schwartz, Scott / Scott, Carol / Seaman, Steven / Searle, Steve / Sharpe, Ted / Sheridan, Andrew / Shownkeen, Ratna / Sims, Sarah / Singer, Jonathan B / Slater, Guy / Smit, Arian / Smith, Douglas R / Spencer, Brian / Stabenau, Arne / Stange-Thomann, Nicole / Sugnet, Charles / Suyama, Mikita / Tesler, Glenn / Thompson, Johanna / Torrents, David / Trevaskis, Evanne / Tromp, John / Ucla, Catherine / Ureta-Vidal, Abel / Vinson, Jade P / Von Niederhausern, Andrew C / Wade, Claire M / Wall, Melanie / Weber, Ryan J / Weiss, Robert B / Wendl, Michael C / West, Anthony P / Wetterstrand, Kris / Wheeler, Raymond / Whelan, Simon / Wierzbowski, Jamey / Willey, David / Williams, Sophie / Wilson, Richard K / Winter, Eitan / Worley, Kim C / Wyman, Dudley / Yang, Shan / Yang, Shiaw-Pyng / Zdobnov, Evgeny M / Zody, Michael C / Lander, Eric S

Nature

2003 Volume 420, Issue 6915, Page(s) 520–562

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality ... ...

Abstract	The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
MeSH term(s)	Animals ; Base Composition ; Chromosomes, Mammalian/genetics ; Conserved Sequence/genetics ; CpG Islands/genetics ; Evolution, Molecular ; Gene Expression Regulation ; Genes/genetics ; Genetic Variation/genetics ; Genome ; Genome, Human ; Genomics ; Humans ; Mice/classification ; Mice/genetics ; Mice, Knockout ; Mice, Transgenic ; Models, Animal ; Multigene Family/genetics ; Mutagenesis ; Neoplasms/genetics ; Physical Chromosome Mapping ; Proteome/genetics ; Pseudogenes/genetics ; Quantitative Trait Loci/genetics ; RNA, Untranslated/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Sex Chromosomes/genetics ; Species Specificity ; Synteny
Chemical Substances	Proteome ; RNA, Untranslated
Language	English
Publishing date	2003-11-26
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature01262
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Elsik, Christine G / Tellam, Ross L / Worley, Kim C / Gibbs, Richard A / Muzny, Donna M / Weinstock, George M / Adelson, David L / Eichler, Evan E / Elnitski, Laura / Guigó, Roderic / Hamernik, Debora L / Kappes, Steve M / Lewin, Harris A / Lynn, David J / Nicholas, Frank W / Reymond, Alexandre / Rijnkels, Monique / Skow, Loren C / Zdobnov, Evgeny M /

Schook, Lawrence / Womack, James / Alioto, Tyler / Antonarakis, Stylianos E / Astashyn, Alex / Chapple, Charles E / Chen, Hsiu-Chuan / Chrast, Jacqueline / Câmara, Francisco / Ermolaeva, Olga / Henrichsen, Charlotte N / Hlavina, Wratko / Kapustin, Yuri / Kiryutin, Boris / Kitts, Paul / Kokocinski, Felix / Landrum, Melissa / Maglott, Donna / Pruitt, Kim / Sapojnikov, Victor / Searle, Stephen M / Solovyev, Victor / Souvorov, Alexandre / Ucla, Catherine / Wyss, Carine / Anzola, Juan M / Gerlach, Daniel / Elhaik, Eran / Graur, Dan / Reese, Justin T / Edgar, Robert C / McEwan, John C / Payne, Gemma M / Raison, Joy M / Junier, Thomas / Kriventseva, Evgenia V / Eyras, Eduardo / Plass, Mireya / Donthu, Ravikiran / Larkin, Denis M / Reecy, James / Yang, Mary Q / Chen, Lin / Cheng, Ze / Chitko-McKown, Carol G / Liu, George E / Matukumalli, Lakshmi K / Song, Jiuzhou / Zhu, Bin / Bradley, Daniel G / Brinkman, Fiona S L / Lau, Lilian P L / Whiteside, Matthew D / Walker, Angela / Wheeler, Thomas T / Casey, Theresa / German, J Bruce / Lemay, Danielle G / Maqbool, Nauman J / Molenaar, Adrian J / Seo, Seongwon / Stothard, Paul / Baldwin, Cynthia L / Baxter, Rebecca / Brinkmeyer-Langford, Candice L / Brown, Wendy C / Childers, Christopher P / Connelley, Timothy / Ellis, Shirley A / Fritz, Krista / Glass, Elizabeth J / Herzig, Carolyn T A / Iivanainen, Antti / Lahmers, Kevin K / Bennett, Anna K / Dickens, C Michael / Gilbert, James G R / Hagen, Darren E / Salih, Hanni / Aerts, Jan / Caetano, Alexandre R / Dalrymple, Brian / Garcia, Jose Fernando / Gill, Clare A / Hiendleder, Stefan G / Memili, Erdogan / Spurlock, Diane / Williams, John L / Alexander, Lee / Brownstein, Michael J / Guan, Leluo / Holt, Robert A / Jones, Steven J M / Marra, Marco A / Moore, Richard / Moore, Stephen S / Roberts, Andy / Taniguchi, Masaaki / Waterman, Richard C / Chacko, Joseph / Chandrabose, Mimi M / Cree, Andy / Dao, Marvin Diep / Dinh, Huyen H / Gabisi, Ramatu Ayiesha / Hines, Sandra / Hume, Jennifer / Jhangiani, Shalini N / Joshi, Vandita / Kovar, Christie L / Lewis, Lora R / Liu, Yih-Shin / Lopez, John / Morgan, Margaret B / Nguyen, Ngoc Bich / Okwuonu, Geoffrey O / Ruiz, San Juana / Santibanez, Jireh / Wright, Rita A / Buhay, Christian / Ding, Yan / Dugan-Rocha, Shannon / Herdandez, Judith / Holder, Michael / Sabo, Aniko / Egan, Amy / Goodell, Jason / Wilczek-Boney, Katarzyna / Fowler, Gerald R / Hitchens, Matthew Edward / Lozado, Ryan J / Moen, Charles / Steffen, David / Warren, James T / Zhang, Jingkun / Chiu, Readman / Schein, Jacqueline E / Durbin, K James / Havlak, Paul / Jiang, Huaiyang / Liu, Yue / Qin, Xiang / Ren, Yanru / Shen, Yufeng / Song, Henry / Bell, Stephanie Nicole / Davis, Clay / Johnson, Angela Jolivet / Lee, Sandra / Nazareth, Lynne V / Patel, Bella Mayurkumar / Pu, Ling-Ling / Vattathil, Selina / Williams, Rex Lee / Curry, Stacey / Hamilton, Cerissa / Sodergren, Erica / Wheeler, David A / Barris, Wes / Bennett, Gary L / Eggen, André / Green, Ronnie D / Harhay, Gregory P / Hobbs, Matthew / Jann, Oliver / Keele, John W / Kent, Matthew P / Lien, Sigbjørn / McKay, Stephanie D / McWilliam, Sean / Ratnakumar, Abhirami / Schnabel, Robert D / Smith, Timothy / Snelling, Warren M / Sonstegard, Tad S / Stone, Roger T / Sugimoto, Yoshikazu / Takasuga, Akiko / Taylor, Jeremy F / Van Tassell, Curtis P / Macneil, Michael D / Abatepaulo, Antonio R R / Abbey, Colette A / Ahola, Virpi / Almeida, Iassudara G / Amadio, Ariel F / Anatriello, Elen / Bahadue, Suria M / Biase, Fernando H / Boldt, Clayton R / Carroll, Jeffery A / Carvalho, Wanessa A / Cervelatti, Eliane P / Chacko, Elsa / Chapin, Jennifer E / Cheng, Ye / Choi, Jungwoo / Colley, Adam J / de Campos, Tatiana A / De Donato, Marcos / Santos, Isabel K F de Miranda / de Oliveira, Carlo J F / Deobald, Heather / Devinoy, Eve / Donohue, Kaitlin E / Dovc, Peter / Eberlein, Annett / Fitzsimmons, Carolyn J / Franzin, Alessandra M / Garcia, Gustavo R / Genini, Sem / Gladney, Cody J / Grant, Jason R / Greaser, Marion L / Green, Jonathan A / Hadsell, Darryl L / Hakimov, Hatam A / Halgren, Rob / Harrow, Jennifer L / Hart, Elizabeth A / Hastings, Nicola / Hernandez, Marta / Hu, Zhi-Liang / Ingham, Aaron / Iso-Touru, Terhi / Jamis, Catherine / Jensen, Kirsty / Kapetis, Dimos / Kerr, Tovah / Khalil, Sari S / Khatib, Hasan / Kolbehdari, Davood / Kumar, Charu G / Kumar, Dinesh / Leach, Richard / Lee, Justin C-M / Li, Changxi / Logan, Krystin M / Malinverni, Roberto / Marques, Elisa / Martin, William F / Martins, Natalia F / Maruyama, Sandra R / Mazza, Raffaele / McLean, Kim L / Medrano, Juan F / Moreno, Barbara T / Moré, Daniela D / Muntean, Carl T / Nandakumar, Hari P / Nogueira, Marcelo F G / Olsaker, Ingrid / Pant, Sameer D / Panzitta, Francesca / Pastor, Rosemeire C P / Poli, Mario A / Poslusny, Nathan / Rachagani, Satyanarayana / Ranganathan, Shoba / Razpet, Andrej / Riggs, Penny K / Rincon, Gonzalo / Rodriguez-Osorio, Nelida / Rodriguez-Zas, Sandra L / Romero, Natasha E / Rosenwald, Anne / 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Science (New York, N.Y.)

2009 Volume 324, Issue 5926, Page(s) 522–528

Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which ... ...

Abstract	To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
MeSH term(s)	Alternative Splicing ; Animals ; Animals, Domestic ; Biological Evolution ; Cattle ; Evolution, Molecular ; Female ; Genetic Variation ; Genome ; Humans ; Male ; MicroRNAs/genetics ; Molecular Sequence Data ; Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Synteny
Chemical Substances	MicroRNAs ; Proteins
Language	English
Publishing date	2009-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1169588
Database	MEDical Literature Analysis and Retrieval System OnLINE

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