Church_2009_PLoS.Biol_7_e1000112

Reference

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.

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 , mouse-cb069

Related information

Gene_locus 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    mouse-cb069

Citations formats

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 (2009)
Lineage-specific biology revealed by a finished genome assembly of the mouse
PLoS Biol 7 :e1000112

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 (2009)
PLoS Biol 7 :e1000112