<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <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 <italic>Brassica rapa</italic>. 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
<italic>Brassica</italic> chromosome 1 revealed their homeologous partner regions on the <italic>Arabidopsis</italic>
genome and a syntenic comparative map between <italic>Brassica</italic> chromosome 1 and
<italic>Arabidopsis</italic> chromosomes. <italic>In silico</italic> 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 <italic>Arabidopsis</italic> chromosomal region reveal overall co-linearity, with 82% sequence
similarity. The data indicate that the <italic>Brassica</italic> genome has undergone triplication and
subsequent gene losses after the divergence of <italic>Arabidopsis</italic> and <italic>Brassica</italic>. Based on in-depth
comparative genome analyses, we propose a comparative genomics approach
for conquering the <italic>Brassica</italic> 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>
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Comp Funct Genomics. 2005 Apr; 6(3):138-146