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Yang, Tae-Jin,Kim, Jung-Sun,Lim, Ki-Byung,Kwon, Soo-Jin,Kim, Jin-A,Jin, Mina,Park, Jee Young,Lim, Myung-Ho,Kim, Ho-Il,Kim, Seog Hyung,Lim, Yong Pyo,Park, Beom-Seok Hindawi Publishing Corporation 2005 Comparative and functional genomics Vol.6 No.3
<P>A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) of <I>Brassica rapa</I>. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones from <I>Brassica</I> chromosome 1 revealed their homeologous partner regions on the <I>Arabidopsis</I> genome and a syntenic comparative map between <I>Brassica</I> chromosome 1 and <I>Arabidopsis</I> chromosomes. <I>In silico</I> chromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (peri)centromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and an <I>Arabidopsis</I> chromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that the <I>Brassica</I> genome has undergone triplication and subsequent gene losses after the divergence of <I>Arabidopsis</I> and <I>Brassica</I>. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering the <I>Brassica</I> genome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100 000 BAC clones. The sequences have been submitted to GenBank with accession numbers: 10 204 BAC ends of the KBrH library (CW978640–CW988843); KBrH138P04, AC155338; KBrH117N09, AC155337; KBrH097M21, AC155348; KBrH093K03, AC155347; KBrH081N08, AC155346; KBrH080L24, AC155345; KBrH077A05, AC155343; KBrH020D15, AC155340; KBrH015H17, AC155339; KBrH001H24, AC155335; KBrH080A08, AC155344; KBrH004D11, AC155341; KBrH117M18, AC146875; KBrH052O08, AC155342.</P>