Bult CJ

References (3)

Title : Lineage-specific biology revealed by a finished genome assembly of the mouse - Church_2009_PLoS.Biol_7_e1000112
Author(s) : Church DM , Goodstadt L , Hillier LW , Zody MC , Goldstein S , She X , Bult CJ , Agarwala R , Cherry JL , DiCuccio M , Hlavina W , Kapustin Y , Meric P , Maglott D , Birtle Z , Marques AC , Graves T , Zhou S , Teague B , Potamousis K , Churas C , Place M , Herschleb J , Runnheim R , Forrest D , Amos-Landgraf J , Schwartz DC , Cheng Z , Lindblad-Toh K , Eichler EE , Ponting CP
Ref : PLoS Biol , 7 :e1000112 , 2009
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.
ESTHER : Church_2009_PLoS.Biol_7_e1000112
PubMedSearch : Church_2009_PLoS.Biol_7_e1000112
PubMedID: 19468303
Gene_locus related to this paper: mouse-1neur , mouse-2neur , mouse-abd12 , mouse-abhd3 , mouse-abhd5 , mouse-acnt1 , mouse-adcl3 , mouse-bphl , mouse-c1ib , mouse-cauxin , mouse-Ces1a , mouse-Ces1b , mouse-Ces1c , mouse-Ces1e , mouse-Ces1h , mouse-Ces2a , mouse-Ces2c , mouse-Ces2f , mouse-Ces2g , mouse-Ces2h , mouse-Ces3b , mouse-Ces4a , mouse-CMBL , mouse-Dorz1 , mouse-DPP6 , mouse-dpp10 , mouse-ephx4 , mouse-g3uzn6 , mouse-KFA , mouse-LIPN , mouse-Lipo2 , mouse-Lipo4 , mouse-MEST , mouse-ndr1 , mouse-ndr4 , mouse-notum , mouse-q3uuq7 , mouse-Q8C1A9 , mouse-Q9DAI6 , mouse-SERHL , mouse-Tex30 , mouse-thyro , mouse-tmco4 , mouse-b1avu7 , mouse-b2rwd2 , mouse-j3qpi0 , mouse-w4vsp6 , mouse-f172a , mouse-f6yqt7

Title : The minimal gene complement of Mycoplasma genitalium - Fraser_1995_Science_270_397
Author(s) : Fraser CM , Gocayne JD , White O , Adams MD , Clayton RA , Fleischmann RD , Bult CJ , Kerlavage AR , Sutton G , Kelley JM , Fritchman RD , Weidman JF , Small KV , Sandusky M , Fuhrmann J , Nguyen D , Utterback TR , Saudek DM , Phillips CA , Merrick JM , Tomb JF , Dougherty BA , Bott KF , Hu PC , Lucier TS , Peterson SN , Smith HO , Hutchison CA, 3rd , Venter JC
Ref : Science , 270 :397 , 1995
Abstract : The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
ESTHER : Fraser_1995_Science_270_397
PubMedSearch : Fraser_1995_Science_270_397
PubMedID: 7569993
Gene_locus related to this paper: mycge-esl1 , mycge-esl2 , mycge-esl3 , mycge-pip

Title : Whole-genome random sequencing and assembly of Haemophilus influenzae Rd - Fleischmann_1995_Science_269_496
Author(s) : Fleischmann RD , Adams MD , White O , Clayton RA , Kirkness EF , Kerlavage AR , Bult CJ , Tomb JF , Dougherty BA , Merrick JM , McKenney K , Sutton G , FitzHugh W , Fields C , Gocayne JD , Scott J , Shirley R , Liu LI , Glodek A , Kelley JM , Weidman JF , Phillips CA , Spriggs T , Hedblom E , Cotton MD , Utterback TR , Hanna MC , Nguyen DT , Saudek DM , Brandon RC , FineLD , Fritchman JL , Fuhrmann JL , Geoghagen NS , Gnehm CL , McDonald LA , Keith V , Small KV , Fraser CM , Smith HO , Venter JC
Ref : Science , 269 :496 , 1995
Abstract : An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
ESTHER : Fleischmann_1995_Science_269_496
PubMedSearch : Fleischmann_1995_Science_269_496
PubMedID: 7542800
Gene_locus related to this paper: haein-HI0193 , haein-metx , haein-pldb , haein-sfgh , haein-y1552 , haein-yfbb