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Article ; Online: Functional annotation of novel lineage-specific genes using co-expression and promoter analysis.

Kumar, Charu G / Everts, Robin E / Loor, Juan J / Lewin, Harris A

BMC genomics

2010 Volume 11, Page(s) 161

Abstract: Background: The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage- ... ...

Abstract	Background: The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis. Results: Clusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development. Conclusions: The placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.
MeSH term(s)	Animals ; Binding Sites/genetics ; Cattle ; Cluster Analysis ; Evolution, Molecular ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Library ; Gene Regulatory Networks ; Liver/metabolism ; Placenta/metabolism ; Pregnancy ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; Thymus Gland/metabolism ; Time Factors ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2010-03-09
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-11-161
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Article ; Online: Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

Loor Juan J / Everts Robin E / Kumar Charu G / Lewin Harris A

BMC Genomics, Vol 11, Iss 1, p

2010 Volume 161

Abstract: Abstract Background The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and ... ...

Abstract	Abstract Background The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis. Results Clusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development. Conclusions The placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.
Keywords	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
Subject code	572
Language	English
Publishing date	2010-03-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article ; Online: Discovery and characterization of 91 novel transcripts expressed in cattle placenta.

Kumar, Charu G / Larson, Joshua H / Band, Mark R / Lewin, Harris A

BMC genomics

2007 Volume 8, Page(s) 113

Abstract: Background: Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian ...

Abstract	Background: Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions. Results: A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions. Conclusion: The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.
MeSH term(s)	Alternative Splicing/genetics ; Animals ; Base Sequence ; Cattle/genetics ; Cattle/metabolism ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Gene Library ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames/genetics ; Placenta/metabolism ; RNA, Messenger/metabolism ; Sequence Analysis, DNA
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2007-05-09
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-8-113
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Article ; Online: Discovery and characterization of 91 novel transcripts expressed in cattle placenta

Band Mark R / Larson Joshua H / Kumar Charu G / Lewin Harris A

BMC Genomics, Vol 8, Iss 1, p

2007 Volume 113

Abstract: Abstract Background Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong ... ...

Abstract	Abstract Background Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions. Results A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions. Conclusion The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.
Keywords	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
Subject code	572
Language	English
Publishing date	2007-05-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article ; Online: ESTIMA, a tool for EST management in a multi-project environment.

Kumar, Charu G / LeDuc, Richard / Gong, George / Roinishivili, Levan / Lewin, Harris A / Liu, Lei

BMC bioinformatics

2004 Volume 5, Page(s) 176

Abstract: Background: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. ...

Abstract	Background: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. Results: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. Conclusions: The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.
MeSH term(s)	Animals ; Bees/genetics ; Catfishes/genetics ; Cattle ; Databases, Genetic ; Expressed Sequence Tags ; Genes, Plant ; Honey ; Internet ; Malus/genetics ; Software ; Songbirds/genetics
Language	English
Publishing date	2004-11-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-5-176
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Article ; Online: ESTIMA, a tool for EST management in a multi-project environment

Lewin Harris A / Roinishivili Levan / Gong George / LeDuc Richard / Kumar Charu G / Liu Lei

BMC Bioinformatics, Vol 5, Iss 1, p

2004 Volume 176

Abstract: Abstract Background Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative ...

Abstract	Abstract Background Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. Results A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee ( Apis mellifera ), cattle ( Bos taurus ), songbird ( Taeniopygia guttata ), corn rootworm ( Diabrotica vergifera ), catfish ( Ictalurus punctatus , Ictalurus furcatus ), and apple ( Malus x domestica ). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. Conclusions The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from ...
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	005
Language	English
Publishing date	2004-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Discovery of eight novel divergent homologs expressed in cattle placenta.

Larson, Joshua H / Kumar, Charu G / Everts, Robin E / Green, Cheryl A / Everts-van der Wind, Annelie / Band, Mark R / Lewin, Harris A

Physiological genomics

2006 Volume 25, Issue 3, Page(s) 405–413

Abstract: Ten divergent homologs were identified using a subtractive bioinformatic analysis of 12,614 cattle placenta expressed sequence tags followed by comparative, evolutionary, and gene expression studies. Among the 10 divergent homologs, 8 have not been ... ...

Abstract	Ten divergent homologs were identified using a subtractive bioinformatic analysis of 12,614 cattle placenta expressed sequence tags followed by comparative, evolutionary, and gene expression studies. Among the 10 divergent homologs, 8 have not been identified previously. These were named as follows: cattle cerebrum and skeletal muscle-specific transcript 1 (CSSMST1), cattle intestine-specific transcript 1 (CIST1), hepatitis A virus cellular receptor 1 amino-terminal domain-containing protein (HAVCRNDP), prolactin-related proteins 8, 9, and 11 (PRP8, PRP9, and PRP11, respectively) and secreted and transmembrane protein 1A and 1B (SECTM1A and SECTM1B, respectively). In addition, two previously known divergent genes were identified, trophoblast Kunitz domain protein 1 (TKDP1) and a new splice variant of TKDP4. Nucleotide substitution analysis provided evidence for positive selection in members of the PRP gene family, SECTM1A and SECTM1B. Gene expression profiles, motif predictions, and annotations of homologous sequences indicate immunological and reproductive functions of the divergent homologs. The genes identified in this study are thus of evolutionary and physiological importance and may have a role in placental adaptations.
MeSH term(s)	Amino Acid Sequence ; Animals ; Cattle/genetics ; Computational Biology/methods ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Mice ; Models, Genetic ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Pan troglodytes/genetics ; Placenta/metabolism ; Pregnancy Proteins/chemistry ; Pregnancy Proteins/genetics ; Pregnancy Proteins/metabolism ; Radiation Hybrid Mapping ; Sequence Alignment ; Sequence Homology, Amino Acid
Chemical Substances	Pregnancy Proteins
Language	English
Publishing date	2006-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2038823-8
ISSN	1531-2267 ; 1094-8341
ISSN (online)	1531-2267
ISSN	1094-8341
DOI	10.1152/physiolgenomics.00307.2005
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Article: A 7872 cDNA microarray and its use in bovine functional genomics.

Everts, Robin E / Band, Mark R / Liu, Z Lewis / Kumar, Charu G / Liu, Lei / Loor, Juan J / Oliveira, Rosane / Lewin, Harris A

Veterinary immunology and immunopathology

2005 Volume 105, Issue 3-4, Page(s) 235–245

Abstract: The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human ...

Abstract	The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, thereby facilitating data analysis and interpretation. A total of 3244 genes were annotated with GO terms. The array is rich in sequences encoding transcription factors, signal transducers and cell cycle regulators. Current research being conducted with this array is described, and an overview of planned improvements in our microarray platform for cattle functional genomics is presented.
MeSH term(s)	Animals ; Cattle/genetics ; Gene Expression/physiology ; Gene Expression Profiling/veterinary ; Genomics/methods ; Oligonucleotide Array Sequence Analysis/veterinary
Language	English
Publishing date	2005-05-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	754160-0
ISSN	1873-2534 ; 0165-2427
ISSN (online)	1873-2534
ISSN	0165-2427
DOI	10.1016/j.vetimm.2005.02.003
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Article: Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

Whitfield, Charles W / Band, Mark R / Bonaldo, Maria F / Kumar, Charu G / Liu, Lei / Pardinas, Jose R / Robertson, Hugh M / Soares, M Bento / Robinson, Gene E

Genome research

2002 Volume 12, Issue 4, Page(s) 555–566

Abstract: To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and ... ...

Abstract	To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains. These sequences were processed to identify 15,311 high-quality ESTs representing 8912 putative transcripts. Putative transcripts were functionally annotated (using the Gene Ontology classification system) based on matching gene sequences in Drosophila melanogaster. The brain ESTs represent a broad range of molecular functions and biological processes, with neurobiological classifications particularly well represented. Roughly half of Drosophila genes currently implicated in synaptic transmission and/or behavior are represented in the Apis EST set. Of Apis sequences with open reading frames of at least 450 bp, 24% are highly diverged with no matches to known protein sequences. Additionally, over 100 Apis transcript sequences conserved with other organisms appear to have been lost from the Drosophila genome. DNA microarrays were fabricated with over 7000 EST cDNA clones putatively representing different transcripts. Using probe derived from single bee brain mRNA, microarrays detected gene expression for 90% of Apis cDNAs two standard deviations greater than exogenous control cDNAs. [The sequence data described in this paper have been submitted to Genbank data library under accession nos. BI502708-BI517278. The sequences are also available at http://titan.biotec.uiuc.edu/bee/honeybee_project.htm.]
MeSH term(s)	Animals ; Bees/genetics ; Behavior, Animal ; Brain Chemistry/genetics ; Computational Biology/methods ; DNA, Complementary/biosynthesis ; DNA, Complementary/genetics ; Drosophila melanogaster/genetics ; Expressed Sequence Tags ; Gene Expression Profiling/methods ; Genes, Insect/genetics ; Genes, Insect/physiology ; Genetics, Behavioral/methods ; Genomics/methods ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/methods
Chemical Substances	DNA, Complementary
Language	English
Publishing date	2002-04
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.5302
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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, 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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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