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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>
Lim, Ki‐,Byung,Yang, Tae‐,Jin,Hwang, Yoon‐,Jung,Kim, Jung Sun,Park, Jee‐,Young,Kwon, Soo‐,Jin,Kim, JinA,Choi, Beom‐,Soon,Lim, Myung‐,Ho,Jin, Mina,Kim, Ho Blackwell Publishing Ltd 2007 The Plant journal Vol.49 No.2
<P><B>Summary</B></P><P>We report the identification and characterization of the major repeats in the centromeric and peri‐centromeric heterochromatin of <I>Brassica rapa.</I> The analysis involved the characterization of 88 629 bacterial artificial chromosomes (BAC) end sequences and the complete sequences of two BAC clones. We identified centromere‐specific retrotransposons of <I>Brassica</I> (CRB) and various peri‐centromere‐specific retrotransposons (PCRBr). Three copies of the CRB were identified in one BAC clone as nested insertions within a tandem array of 24 copies of a 176 bp centromeric repeat, CentBr. A complex mosaic structure consisting of nine PCRBr elements and large blocks of 238 bp degenerate tandem repeats (TR238) were found in or near a derivative of 5S–25S rDNA sequences. The chromosomal positions of selected repeats were determined using <I>in situ</I> hybridization. These revealed that CRB is a major component of all centromeres in three diploid <I>Brassica</I> species and their allotetraploid relatives. However, CentBr was not detected in the most distantly related of the diploid species analyzed, <I>B. nigra</I>. PCRBr and TR238 were found to be major components in the peri‐centromeric heterochromatin blocks of four chromosomes of <I>B. rapa.</I> These repetitive elements were not identified in <I>B. oleracea</I> or <I>B. nigra</I>, indicating that they are A‐genome‐specific.</P>