Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa
Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa
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DOI：
10.1007/s00438-003-0844-0
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发表时间：
2003-06-01
影响因子：
3.1
通讯作者：
Nishio, T
中科院分区：
文献类型：
--
作者：
Fukai, E;Fujimoto, R;Nishio, T
测定了芜菁S-60（II类S单倍型）的SP11、SRK和SLG基因的86.4 kb区域的核苷酸序列。在测序区域中，除了SP11-60、SRK-60和SLG-60外，还发现了13个可能的基因。这些序列中有5个是以cDNA形式分离的，5个是已知基因、cDNA或ORF的同源物，3个是假设的ORF。然而，基于它们的核苷酸序列，其中一些被认为是无功能的。鉴定了II类S-60和芸苔属I类S单倍型之间的两个共线性区域，即，S侧翼区1显示非基因序列的部分共线性，S侧翼区2显示高水平的共线性。所观察到的共线性使得有可能比较SP-11，SRK，和SLG基因在S位点之间的5个测序的S单倍型的顺序。结果表明，II类S-60中SRK和SLG的顺序与迄今为止报道的四种I类S单倍型中的顺序相反，SP11、SRK和SLG的顺序与I类S-910中的顺序相反。SAN 1（S locus Anther-expressed Non-coding RNA like-1）基因位于SP11-60和SRK-60之间，具有非编码RNA（ncRNA）基因的特征，但在数据库中未发现同源序列。该序列在花药中转录，但在柱头或叶中不转录。这些功能的S-60的基因组结构进行了讨论，特别提到II类S单倍型的特点。
The nucleotide sequence of an 86.4-kb region that includes the SP11, SRK, and SLG genes of Brassica rapa S-60 (a class-II S haplotype) was determined. In the sequenced region, 13 putative genes were found besides SP11-60, SRK-60, and SLG-60. Five of these sequences were isolated as cDNAs, five were homologues of known genes, cDNAs, or ORFs, and three are hypothetical ORFs. Based on their nucleotide sequences, however, some of them are thought to be non-functional. Two regions of colinearity between the class-II S-60 and Brassica class-I S haplotypes were identified, i.e., S flanking region 1 which shows partial colinearity of non-genic sequences and S flanking region 2 which shows a high level of colinearity. The observed colinearity made it possible to compare the order of SP-11, SRK, and SLG genes in the S locus between the five sequenced S haplotypes. It emerged that the order of SRK and SLG in class-II S-60is the reverse of that in the four class-I S haplotypes reported so far, and the order of SP11, SRK and SLG is the opposite of that in the class-I haplotype S-910. The possible gene designated as SAN1 ( S locus Anther-expressed Non-coding RNA like-1), which is located in the region between SP11-60 and SRK-60, has features reminiscent of genes for non-coding RNAs (ncRNAs), but no homologous sequences were found in the databases. This sequence is transcribed in anthers but not in stigmas or leaves. These features of the genomic structure of S-60 are discussed with special reference to the characteristics of class-II S haplotypes.