Ahsan B

References (2)

Title : The genome of a lepidopteran model insect, the silkworm Bombyx mori - Xia_2008_Insect.Biochem.Mol.Biol_38_1036
Author(s) : Xia Q , Wang J , Zhou Z , Li R , Fan W , Cheng D , Cheng T , Qin J , Duana J , Xu H , Li Q , Li N , Wang M , Dai F , Liu C , Lin Y , Zhao P , Zhang H , Liu S , Zha X , Li C , Zhao A , Pan M , Pan G , Shen Y , Gao Z , Wang Z , Wang G , Wu Z , Hou Y , Chai C , Yu Q , He N , Zhang Z , Li S , Yang H , Lu C , Xiang Z , Mita K , Kasahara M , Nakatani Y , Yamamoto K , Abe H , Ahsan B , Daimoni T , Doi K , Fujii T , Fujiwara H , Fujiyama A , Futahashi R , Hashimotol S , Ishibashi J , Iwami M , Kadono-Okuda K , Kanamori H , Kataoka H , Katsuma S , Kawaoka S , Kawasaki H , Kohara Y , Kozaki T , Kuroshu RM , Kuwazaki S , Matsushima K , Minami H , Nagayasu Y , Nakagawa T , Narukawa J , Nohata J , Ohishi K , Ono Y , Osanai-Futahashi M , Ozaki K , Qu W , Roller L , Sasaki S , Sasaki T , Seino A , Shimomura M , Shin-I T , Shinoda T , Shiotsuki T , Suetsugu Y , Sugano S , Suwa M , Suzuki Y , Takiya S , Tamura T , Tanaka H , Tanaka Y , Touhara K , Yamada T , Yamakawa M , Yamanaka N , Yoshikawa H , Zhong YS , Shimada T , Morishita S
Ref : Insect Biochemistry & Molecular Biology , 38 :1036 , 2008
Abstract : Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.
ESTHER : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedSearch : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedID: 19121390
Gene_locus related to this paper: bommo-a0mnw6 , bommo-a1yw85 , bommo-a9ls22 , bommo-ACHE1 , bommo-ACHE2 , bommo-b0fgv8 , bommo-b1q137 , bommo-b1q139 , bommo-b1q140 , bommo-b1q141 , bommo-b2zdz0 , bommo-b3gef6 , bommo-b3gef7 , bommo-b3gs55 , bommo-b3gs56 , bommo-d2ktu3 , bommo-d2ktu5 , bommo-d9ile0 , bommo-e1cga5 , bommo-e1cga6 , bommo-g8fpz6 , bommo-h9iu43 , bommo-h9iu46 , bommo-h9iu47.1 , bommo-h9iu47.2 , bommo-h9iue5 , bommo-h9ivg2 , bommo-h9iwj7 , bommo-h9iwj8 , bommo-h9ix58 , bommo-h9ixi1.1 , bommo-h9ixi1.2 , bommo-h9iy47 , bommo-h9izw1 , bommo-h9j0s4 , bommo-h9j1y0 , bommo-h9j3r0 , bommo-h9j3w6 , bommo-h9j3w7 , bommo-h9j5t0 , bommo-h9j8g3 , bommo-h9j9k9 , bommo-h9j066 , bommo-h9j067 , bommo-h9j593 , bommo-h9j594 , bommo-h9j990 , bommo-h9jde8 , bommo-h9jde9 , bommo-h9jdf0 , bommo-h9jds4 , bommo-h9jle7 , bommo-h9jn83 , bommo-h9jn85 , bommo-h9jrg2 , bommo-h9jyh9 , bommo-JHE , bommo-m1rmh6 , bommo-q1hq05 , bommo-q4tte1 , bommo-h9j592 , bommo-h9j604 , bommo-h9jpm8 , bommo-h9iss4 , bommo-h9j2c7

Title : The medaka draft genome and insights into vertebrate genome evolution - Kasahara_2007_Nature_447_714
Author(s) : Kasahara M , Naruse K , Sasaki S , Nakatani Y , Qu W , Ahsan B , Yamada T , Nagayasu Y , Doi K , Kasai Y , Jindo T , Kobayashi D , Shimada A , Toyoda A , Kuroki Y , Fujiyama A , Sasaki T , Shimizu A , Asakawa S , Shimizu N , Hashimoto S , Yang J , Lee Y , Matsushima K , Sugano S , Sakaizumi M , Narita T , Ohishi K , Haga S , Ohta F , Nomoto H , Nogata K , Morishita T , Endo T , Shin IT , Takeda H , Morishita S , Kohara Y
Ref : Nature , 447 :714 , 2007
Abstract : Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.
ESTHER : Kasahara_2007_Nature_447_714
PubMedSearch : Kasahara_2007_Nature_447_714
PubMedID: 17554307
Gene_locus related to this paper: fugru-3cxest , fugru-4cxest , fugru-4neur , fugru-ACHE , fugru-ACHEE , fugru-balip , fugru-BCHE , fugru-BCHEB , fugru-cxest , oryla-ACHE , oryla-BCHE , oryla-d2x2i4 , oryla-h2m6h1 , oryla-h2m7w4 , oryla-h2m361 , oryla-h2mbn6 , oryla-h2mfw1 , oryla-h2mhi0 , oryla-h2mhl7 , oryla-h2mpb5 , oryla-h2mqz5 , oryla-h2mvs7 , oryla-h2mz49 , oryla-h2n1l9 , oryla-nlgn2 , takru-1neur , takru-2bneur , takru-3bneur , takru-h2rke7 , takru-h2rmg3 , takru-h2rsj9 , takru-h2rw77 , takru-h2ryq0 , takru-h2sci9 , takru-h2se90 , takru-h2spg7 , takru-h2sxi1 , takru-h2ts55 , takru-h2ts56 , takru-h2uxa9 , takru-h2vaf1 , takru-nlgn2a , takru-nlgn3a , takru-nlgn4a , oryla-h2mff8 , oryla-h2m2f0 , oryla-h2ler5 , takru-h2tsm6 , takru-h2tq49 , takru-h2tq47 , takru-h2s286 , takru-h2tng4 , takru-h2tq50 , takru-h2tng3 , takru-h2tng2 , oryla-h2lj38 , oryla-h2mxe6 , takru-h2tq48 , oryla-h2lf11 , takru-h2u5j0 , takru-h2rpm8 , oryla-h2n273 , oryla-h2n271 , oryla-h2lum7 , takru-h2tpz2 , takru-h2u3j1 , oryla-h2mdv3 , takru-h2tzm9 , takru-h2u8u6 , oryla-h2lcw8 , oryla-h2lc35 , oryla-h2ln66 , oryla-h2m8k0 , oryla-h2mdj7 , oryla-h2lw61 , oryla-h2lxe3 , oryla-h2l8y7 , oryla-h2mr84 , oryla-h2mr95 , oryla-h2mcz6 , oryla-h2lxr5 , oryla-h2ly57 , oryla-a0a3p9kz03 , oryla-a0a3p9hfu1 , oryla-h2m307 , oryla-h2lch5 , oryla-h2ldw9 , oryla-a0a3b3ic40 , oryla-h2ldi5 , oryla-h2mun1 , oryla-a0a3p9jla3