The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
BMC Genomics. 2011 Apr 14;12:188. doi: 10.1186/1471-2164-12-188.
Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding.
To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp.
BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of the zebrafish genome. BES of common carp are tremendous tools for comparative mapping between the two closely related species, zebrafish and common carp, which should facilitate both structural and functional genome analysis in common carp.
鲤鱼是世界上最重要的水产养殖硬骨鱼之一。鲤鱼和其他密切相关的鲤科鱼类提供了世界上超过 30%的水产养殖产量。然而，鲤鱼的基因组资源仍然相对不发达。BAC 末端序列（BES）是 BAC 锚定遗传标记开发、连锁图谱和物理图谱整合以及全基因组序列组装和支架的基因组研究的重要资源。
为了在鲤鱼（Cyprinus carpio）中开发这种有价值的资源，总共对 40224 个 BAC 克隆进行了两端测序，经过序列处理后，生成了 65720 个清洁的 BES，平均读长为 647bp，代表了鲤鱼基因组的 42522168bp 或 2.5%。首次对鲤鱼基因组进行了调查，使用了各种生物信息学工具。鲤鱼基因组含有超过 17.3%的重复序列，GC 含量为 36.8%，有 518 个转座子 ORFs。为了识别和开发 BAC 锚定微卫星标记，从 10355 个 BES 中总共检测到 13581 个微卫星。从 7453 个 BAC 上的 9443 个 BES 中识别出了 7127 个编码区基因，其中 1990 个 BAC 的两端都有基因。为了评估与亲缘关系密切的斑马鱼基因组的相似性，将鲤鱼的 BES 与斑马鱼基因组进行了比对。鲤鱼的 39335 个 BES 在斑马鱼基因组上有保守的同源物，这表明了斑马鱼和鲤鱼基因组之间的高度相似性，表明一旦我们有了鲤鱼的物理图谱，就可以在斑马鱼和鲤鱼之间进行比较图谱。
BAC 末端序列是鲤鱼全基因组首次调查的重要资源。重复 DNA 估计约占鲤鱼基因组的 28%，表明基因组的复杂性较高。比较分析将大约 40000 个 BES 映射到斑马鱼基因组上，并建立了 3100 多个微同线，覆盖了斑马鱼基因组的 50%以上。鲤鱼的 BES 是这两个密切相关的物种，即斑马鱼和鲤鱼之间比较图谱的重要工具，这应该有助于鲤鱼的结构和功能基因组分析。
