Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms.
Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms.
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DOI：
10.1155/2012/437026
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Ezura H
中科院分区：
文献类型：
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作者：
Asamizu E;Shirasawa K;Hirakawa H;Sato S;Tabata S;Yano K;Ariizumi T;Shibata D;Ezura H
从矮化模型番茄 cv. 中生成了总共 93,682 个 BAC 末端序列 (BES)。微型汤姆。删除重复序列后，根据标准品种“Heinz 1706”的参考番茄基因组对 BES 进行相似性搜索。通过参考“Heinz 1706”物理图谱并通过消除冗余或不显着的命中，选择28,804个“独特对末端”和8,263个“独特末端”来构建假设的BAC重叠群。 BAC重叠群的总物理长度为495、833、423bp，覆盖整个基因组的65.3%。常染色质和异染色质的平均覆盖度分别为58.9%和67.3%。通过该分析，确定了两种可能的基因组重排：一种发生在 2 号染色体（倒位），另一种发生在 3 号染色体（倒位和易位）。通过 BLAST 比对鉴定了两个品种之间的多态性（SNP 和 Indel）。结果，171,792 个多态性被定位在 12 条染色体上。其中，在常染色质中发现了 30,930 个多态性（每 3,565bp 1 个），在异染色质中发现了 140,862 个多态性（每 2,737bp 1 个）。基因组中的平均多态性密度为每2,886bp有1个多态性。为了便于在 Micro-Tom 研究中使用这些数据，TOMATOMICS 数据库中提供了 BAC 重叠群和多态性信息。
A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.