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1. Sequence Evaluation of Four Pooled-Tissue Normalized Bovine cDNA Libraries and Construction of a Gene Index for Cattle

Author:
Pertea, Geo,   et al.   ; Smith, Timothy P.L.; Grosse, William M.; Freking, Brad A.; Roberts, Andrew J.; Stone, Roger T.; Casas. Eduardo; Wray, James E.; White, Joseph; Cho, Jennifer; Fahrenkrug, Scott C.; Bennett, Gary L.; Heaton, Michael P.; Laegreid, William W.; Rohrer, Gary A.; Chitko-McKown, Carol G.; Holt, Ingeborg; Karamycheva, Svetlana; Liang, Feng; Quackenbush, John; Keele, John W.;     Show all 21 Authors
Source:
Genome research 2001 v.11 no.4 pp. 626
ISSN:
1549-5469
Subject:
cattle; animal genetics; cDNA libraries; genes; genetic techniques and protocols; animal tissues; beef cattle; nucleotide sequences; expressed sequence tags
Abstract:
... An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high-throughput sequencing. The libraries were made with RNA pooled from multiple tissues to increase eff ...
Handle:
10113/36388
DOI:
10.1101/gr.170101
PubMed:
11282978
PubMed Central:
PMC311058

2. Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus

Author:
Pertea, Geo,   et al.   ; Wang, Minghua; Guerrero, Felix D.; Nene, Vishvanath M.;     Show all 4 Authors
Source:
BMC Genomics 2007 v.8 pp. 368
ISSN:
1471-2164
Subject:
Boophilus microplus; acaricides; cold; conserved sequences; databases; expressed sequence tags; genes; genomics; hosts; larvae; messenger RNA; odors; phylogeny; proteins; stress response; tick control; ticks; transcriptome
Abstract:
... Background: The southern cattle tick, Rhipicephalus (Boophilus) microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks. Results: We present a global comparative genomic analys ...
Handle:
10113/55827
DOI:
10.1186/1471-2164-8-368
PubMed:
17935616
PubMed Central:
PMC2100071

3. A whole-genome assembly of the domestic cow, Bos taurus

Author:
Pertea, Geo,   et al.   ; Zimin, Aleksey V; Delcher, Arthur L; Florea, Liliana; Kelley, David R; Schatz, Michael C; Puiu, Daniela; Hanrahan, Finnian; Van Tassell, Curtis P; Sonstegard, Tad S; Marçais, Guillaume; Roberts, Michael; Subramanian, Poorani; Yorke, James A; Salzberg, Steven L;     Show all 15 Authors
Source:
Genome biology 2009 v.10 no.4 pp. 2192
ISSN:
1474-760X
Subject:
Y chromosome; cows; genome; humans; sequence analysis
Abstract:
... BACKGROUND: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods. RESULTS: We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering mor ...
DOI:
10.1186/gb-2009-10-4-r42
PubMed:
19393038
PubMed Central:
PMC2688933

4. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Author:
Pertea, Geo,   et al.   ; Dalloul, Rami A.; Long, Julie A.; Zimin, Aleksey V.; Aslam, Luqman; Beal, Kathryn; Ann Blomberg, Le; Bouffard, Pascal; Burt, David W.; Crasta, Oswald; Crooijmans, Richard P. M. A.; Cooper, Kristal; Coulombe, Roger A.; De, Supriyo; Delany, Mary E.; Dodgson, Jerry B.; Dong, Jennifer J.; Evans, Clive; Frederickson, Karin M.; Flicek, Paul; Florea, Liliana; Folkerts, Otto; Groenen, Martien A. M.; Harkins, Tim T.; Herrero, Javier; Hoffmann, Steve; Megens, Hendrik-Jan; Jiang, Andrew; de Jong, Pieter; Kaiser, Pete; Kim, Heebal; Kim, Kyu-Won; Kim, Sungwon; Langenberger, David; Lee, Mi-Kyung; Lee, Taeheon; Mane, Shrinivasrao; Marcais, Guillaume; Marz, Manja; McElroy, Audrey P.; Modise, Thero; Nefedov, Mikhail; Notredame, Cédric; Paton, Ian R.; Payne, William S.; Prickett, Dennis; Puiu, Daniela; Qioa, Dan; Raineri, Emanuele; Ruffier, Magali; Salzberg, Steven L.; Schatz, Michael C.; Scheuring, Chantel; Schmidt, Carl J.; Schroeder, Steven; Searle, Stephen M. J.; Smith, Edward J.; Smith, Jacqueline; Sonstegard, Tad S.; Stadler, Peter F.; Tafer, Hakim; Tu, Zhijian (Jake); Van Tassell, Curtis P.; Vilella, Albert J.; Williams, Kelly P.; Yorke, James A.; Zhang, Liqing; Zhang, Hong-Bin; Zhang, Xiaojun; Zhang, Yang; Reed, Kent M.; Roberts, Richard J.;     Show all 72 Authors
ISSN:
1545-7885
Subject:
Meleagris gallopavo; Taeniopygia guttata; chickens; chromosomes; cost effectiveness; evolution; gene deletion; genes; genetic variation; genome assembly; heterozygosity; high-throughput nucleotide sequencing; immune system; mammals; models; non-coding RNA; nucleotide sequences; quantitative traits; turkeys
Abstract:
... A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome ...
DOI:
10.1371/journal.pbio.1000475
PubMed:
20838655
PubMed Central:
PMC2935454

5. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Author:
Pertea, Geo,   et al.   ; Kim, Daehwan; Trapnell, Cole; Pimentel, Harold; Kelley, Ryan; Salzberg, Steven L;     Show all 6 Authors
Source:
Genome biology 2013 v.14 no.4 pp. R36
ISSN:
1474-760X
Subject:
RNA; computer software; genes; nucleotide sequences; sequence alignment; transcriptome
Abstract:
... TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can ali ...
DOI:
10.1186/gb-2013-14-4-r36
PubMed:
23618408
PubMed Central:
PMC4053844