Pertea G

References (5)

Title : First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans) - Luo_2017_G3.(Bethesda)_7_3831
Author(s) : Luo R , Zimin A , Workman R , Fan Y , Pertea G , Grossman N , Wear MP , Jia B , Miller H , Casadevall A , Timp W , Zhang SX , Salzberg SL
Ref : G3 (Bethesda) , 7 :3831 , 2017
Abstract : Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,627,092 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8896 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.
ESTHER : Luo_2017_G3.(Bethesda)_7_3831
PubMedSearch : Luo_2017_G3.(Bethesda)_7_3831
PubMedID: 28963165
Gene_locus related to this paper: 9pezi-a0a2n3nij3 , 9pezi-a0a2n3mzq9 , 9pezi-a0a2n3n7y4

Title : Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis - Dalloul_2010_PLoS.Biol_8_E1000475
Author(s) : Dalloul RA , Long JA , Zimin AV , Aslam L , Beal K , Blomberg Le A , Bouffard P , Burt DW , Crasta O , Crooijmans RP , Cooper K , Coulombe RA , De S , Delany ME , Dodgson JB , Dong JJ , Evans C , Frederickson KM , Flicek P , Florea L , Folkerts O , Groenen MA , Harkins TT , Herrero J , Hoffmann S , Megens HJ , Jiang A , de Jong P , Kaiser P , Kim H , Kim KW , Kim S , Langenberger D , Lee MK , Lee T , Mane S , Marcais G , Marz M , McElroy AP , Modise T , Nefedov M , Notredame C , Paton IR , Payne WS , Pertea G , Prickett D , Puiu D , Qioa D , Raineri E , Ruffier M , Salzberg SL , Schatz MC , Scheuring C , Schmidt CJ , Schroeder S , Searle SM , Smith EJ , Smith J , Sonstegard TS , Stadler PF , Tafer H , Tu ZJ , Van Tassell CP , Vilella AJ , Williams KP , Yorke JA , Zhang L , Zhang HB , Zhang X , Zhang Y , Reed KM
Ref : PLoS Biol , 8 : , 2010
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 assembly ( approximately 1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
ESTHER : Dalloul_2010_PLoS.Biol_8_E1000475
PubMedSearch : Dalloul_2010_PLoS.Biol_8_E1000475
PubMedID: 20838655
Gene_locus related to this paper: melga-g1mv74 , melga-g1myh1 , melga-g1n3b6 , melga-g1n4i8 , melga-g1n8a7 , melga-g1nb53 , melga-g1ndd8 , melga-g1npu5 , melga-g3ur65 , melga-g3uur6 , melga-g1njn8 , melga-g1mrp7 , melga-g1mzw6 , melga-g1n2a7 , melga-g1n608 , melga-g1n2j6 , melga-g1n2k0 , melga-g1ncb6 , melga-g1nei5 , melga-g1n1j3 , melga-g1nfd3 , melga-g1nna9 , melga-h9h0c1 , melga-g1nnl1 , melga-g1nhb9 , melga-g1mtl7 , fical-u3jnn0 , melga-g1n332 , melga-g1mtx9 , melga-g1nns1

Title : A whole-genome assembly of the domestic cow, Bos taurus - Zimin_2009_Genome.Biol_10_R42
Author(s) : Zimin AV , Delcher AL , Florea L , Kelley DR , Schatz MC , Puiu D , Hanrahan F , Pertea G , Van Tassell CP , Sonstegard TS , Marcais G , Roberts M , Subramanian P , Yorke JA , Salzberg SL
Ref : Genome Biol , 10 :R42 , 2009
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 more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions.
CONCLUSIONS: By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome.
ESTHER : Zimin_2009_Genome.Biol_10_R42
PubMedSearch : Zimin_2009_Genome.Biol_10_R42
PubMedID: 19393038
Gene_locus related to this paper: bovin-1lipg , bovin-ABHD16A , bovin-e1ba50 , bovin-e1bbv2 , bovin-e1bkm2 , bovin-e1bnq0 , bovin-e1bnt1 , bovin-e1bpw3 , bovin-f1mcd9 , bovin-f1mps6 , bovin-f1msa3 , bovin-f1n110 , bovin-f1n385 , bovin-hslip , bovin-KANSL3 , bovin-ndrg2 , bovin-q0vck8 , bovin-q2kix6 , bovin-q2ta14 , bovin-q3sz73 , bovin-q3sz79 , bovin-f1n673 , bovin-e1bll5 , bovin-g5e5g5 , bovin-g5e5i3 , bovin-e1bjq9 , bovin-f1mc21 , bovin-a0a3q1nm09 , bovin-a7mb66

Title : Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs - Okazaki_2002_Nature_420_563
Author(s) : Okazaki Y , Furuno M , Kasukawa T , Adachi J , Bono H , Kondo S , Nikaido I , Osato N , Saito R , Suzuki H , Yamanaka I , Kiyosawa H , Yagi K , Tomaru Y , Hasegawa Y , Nogami A , Schonbach C , Gojobori T , Baldarelli R , Hill DP , Bult C , Hume DA , Quackenbush J , Schriml LM , Kanapin A , Matsuda H , Batalov S , Beisel KW , Blake JA , Bradt D , Brusic V , Chothia C , Corbani LE , Cousins S , Dalla E , Dragani TA , Fletcher CF , Forrest A , Frazer KS , Gaasterland T , Gariboldi M , Gissi C , Godzik A , Gough J , Grimmond S , Gustincich S , Hirokawa N , Jackson IJ , Jarvis ED , Kanai A , Kawaji H , Kawasawa Y , Kedzierski RM , King BL , Konagaya A , Kurochkin IV , Lee Y , Lenhard B , Lyons PA , Maglott DR , Maltais L , Marchionni L , McKenzie L , Miki H , Nagashima T , Numata K , Okido T , Pavan WJ , Pertea G , Pesole G , Petrovsky N , Pillai R , Pontius JU , Qi D , Ramachandran S , Ravasi T , Reed JC , Reed DJ , Reid J , Ring BZ , Ringwald M , Sandelin A , Schneider C , Semple CA , Setou M , Shimada K , Sultana R , Takenaka Y , Taylor MS , Teasdale RD , Tomita M , Verardo R , Wagner L , Wahlestedt C , Wang Y , Watanabe Y , Wells C , Wilming LG , Wynshaw-Boris A , Yanagisawa M , Yang I , Yang L , Yuan Z , Zavolan M , Zhu Y , Zimmer A , Carninci P , Hayatsu N , Hirozane-Kishikawa T , Konno H , Nakamura M , Sakazume N , Sato K , Shiraki T , Waki K , Kawai J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Imotani K , Ishii Y , Itoh M , Kagawa I , Miyazaki A , Sakai K , Sasaki D , Shibata K , Shinagawa A , Yasunishi A , Yoshino M , Waterston R , Lander ES , Rogers J , Birney E , Hayashizaki Y
Ref : Nature , 420 :563 , 2002
Abstract : Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
ESTHER : Okazaki_2002_Nature_420_563
PubMedSearch : Okazaki_2002_Nature_420_563
PubMedID: 12466851
Gene_locus related to this paper: mouse-1lipg , mouse-1llip , mouse-1plrp , mouse-3neur , mouse-ABH15 , mouse-abhd4 , mouse-abhd5 , mouse-Abhd8 , mouse-Abhd11 , mouse-abhda , mouse-acot4 , mouse-adcl4 , mouse-AI607300 , mouse-BAAT , mouse-bphl , mouse-C87498 , mouse-Ldah , mouse-Ces1d , mouse-Ces2e , mouse-CMBL , mouse-DGLB , mouse-dpp9 , mouse-ES10 , mouse-F135A , mouse-FASN , mouse-hslip , mouse-hyes , mouse-Kansl3 , mouse-LIPH , mouse-LIPK , mouse-lipli , mouse-LIPM , mouse-lypla1 , mouse-lypla2 , mouse-MEST , mouse-MGLL , mouse-ndr4 , mouse-OVCA2 , mouse-pafa , mouse-pcp , mouse-ppce , mouse-Ppgb , mouse-PPME1 , mouse-q3uuq7 , mouse-Q8BLF1 , mouse-ACOT6 , mouse-Q8C1A9 , mouse-Q9DAI6 , mouse-Q80UX8 , mouse-Q8BGG9 , mouse-Q8C167 , mouse-rbbp9 , mouse-SERHL , mouse-tssp

Title : Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle - Smith_2001_Genome.Res_11_626
Author(s) : Smith TP , Grosse WM , Freking BA , Roberts AJ , Stone RT , Casas E , Wray JE , White J , Cho J , Fahrenkrug SC , Bennett GL , Heaton MP , Laegreid WW , Rohrer GA , Chitko-McKown CG , Pertea G , Holt I , Karamycheva S , Liang F , Quackenbush J , Keele JW
Ref : Genome Res , 11 :626 , 2001
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 efficiency of normalization and maximize the number of independent genes for which sequence data were obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter- and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed in combination with 56,500 other bovine EST sequences present in the GenBank dbEST database to construct a cattle Gene Index (available from The Institute for Genomic Research at http:\/\/www.tigr.org/tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the Web site. Analysis of individual library sequence data indicates that the pooled-tissue approach was highly effective in preparing libraries for efficient deep sequencing.
ESTHER : Smith_2001_Genome.Res_11_626
PubMedSearch : Smith_2001_Genome.Res_11_626
PubMedID: 11282978
Gene_locus related to this paper: bovin-abhd2 , bovin-abhd4 , bovin-balip , bovin-LPLA2 , bovin-paf2 , bovin-ppme1 , bovin-q5e9h0 , bovin-ABHDA