National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV 25430, USA.
Mar Biotechnol (NY). 2012 Jun;14(3):343-57. doi: 10.1007/s10126-011-9418-z. Epub 2011 Nov 19.
DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.
为了改进虹鳟鱼（Oncorhynchus mykiss）基因组的第一代整合物理图谱和遗传图谱，我们生成了来自两个新文库的细菌人工染色体（BAC）的 DNA 指纹和末端序列。当前的物理图谱版本由 167989 个克隆组成，其中 158670 个组装成了连续序列，9319 个为单序列。连续序列的数量从 4173 个减少到了 3220 个。新文库克隆的末端测序总共生成了 11958 条高质量的序列读段。末端序列被用来开发了 238 个新的微卫星，其中 42 个被添加到了遗传图谱中。使用 188443 个 BAC 末端序列（BES）读段分析了虹鳟鱼基因组与模式鱼类基因组之间的保守同线性。针对斑马鱼、青鳉和棘鱼基因组，BLASTN 比对显著命中的 BES 读段的分数分别为 8.8%、9.7%和 10.5%，而针对斑马鱼、青鳉和棘鱼蛋白数据库的 BLASTX 比对显著命中的分数分别为 6.2%、5.8%和 5.5%。将虹鳟鱼 BES 分组到指纹连续序列中，通过分组鉴定出的保守同线性的独特区域的总数分别为棘鱼、青鳉和斑马鱼的 2259、2229 和 2203 个。这些数字大约是我们之前使用 BAC 配对末端鉴定的三倍到五倍。根据整合的物理图谱和遗传图谱中得出的连锁群对保守同线性分析结果进行聚类，结果表明尽管序列同源性较低，但虹鳟鱼和模式鱼类的染色体臂之间仍然存在大量的宏同线性。
