CIRAD-PERSYST, Aquaculture Research Unit, TA B-20/A, Campus International de Baillarguet, 34398 Montpellier cedex 5, France.
BMC Genomics. 2010 Nov 16;11:636. doi: 10.1186/1471-2164-11-636.
The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.
We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies.
Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.
尼罗罗非鱼是水产养殖中的第二大重要鱼类。它是一种优秀的实验室模型，与以快速物种形成而闻名的非洲湖慈鲷关系密切。该物种已经开发出了一系列基因组资源，包括遗传图谱和 EST。在这里，我们分析 BAC 末端序列以开发比较物理图谱，并估计罗非鱼和其他模式鱼类之间的基因组重排数量。
我们从 106,259 个罗非鱼 BAC 的一个或两个末端获得了序列。针对刺鱼、青鳉和河豚鱼基因组组装的 BLAST 分析，为每个物种确定了大约 25,000 个 BAC 的同源性。我们计算出罗非鱼和这些物种之间的重排断点大约每 3 Mb 发生一次，跨越整个基因组。对先前通过限制性指纹图谱组装成连续序列的 35,000 个克隆进行分析，确定了更长范围的同线性。
我们的数据表明，最近硬骨鱼的染色体进化主要由基因重复的交替丢失和染色体内重排（~每百万年一次）驱动。这些物理图谱是对慈鲷鱼类特征进行比较定位克隆的有用资源。这些克隆的配对 BAC 末端序列将是罗非鱼基因组即将进行的霰弹枪测序组装的重要资源。
