Ruvinskiy Daniil, Larkin Denis M, Farré Marta
Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.
The Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Front Genet. 2019 Feb 5;10:32. doi: 10.3389/fgene.2019.00032. eCollection 2019.
The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the assembly. This dromedary camel assembly will be an invaluable tool to verify future camel assemblies generated with chromatin conformation or/and long read technologies. This study provides the first near-chromosome assembly of the dromedary camel, thus adding this economically important species to a growing pool of knowledge regarding the genome structure of domesticated livestock.
单峰骆驼在世界许多地区都是具有重要经济和社会意义的家畜品种，可用于运输以及产奶和产肉。与牛和马很相似，骆驼既可以在工业化养殖环境中被发现，也用于体育运动。骆驼赛跑是一个价值数百万美元的产业，一些参赛骆驼的价值超过950万美元。尽管单峰骆驼对人类具有明显价值，但在基因组学领域它却是一个被忽视的物种。虽然牛和其他驯化物种在基因组组装方面受到了很多关注，但骆驼的基因组组装仅达到支架水平，这并不能明确显示测序片段的顺序或染色体位置。在本研究中，实施了参考辅助染色体组装（RACA）算法，利用骆驼支架的读对信息，并与牛和人类基因组进行比对，以便在近染色体水平组装中对这些支架进行组织和定向。该方法生成了72个大尺寸片段（N50为54.36 Mb）。然后将这些预测的染色体片段（PCF）与骆驼的比较图谱和羊驼染色体的细胞遗传学图谱进行比较，使我们能够进一步优化组装。这种单峰骆驼组装将成为验证未来利用染色质构象或/和长读长技术生成的骆驼组装的宝贵工具。本研究提供了首个单峰骆驼的近染色体组装，从而将这个具有重要经济意义的物种纳入到关于家畜基因组结构的不断增长的知识宝库中。
