A Near Chromosome Assembly of the Dromedary Camel Genome
A Near Chromosome Assembly of the Dromedary Camel Genome
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DOI：
10.3389/fgene.2019.00032
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发表时间：
2019-02
影响因子：
3.7
通讯作者：
D. Ruvinskiy;D. Larkin;M. Farré
中科院分区：
文献类型：
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作者：
D. Ruvinskiy;D. Larkin;M. Farré
单峰骆驼在世界许多地方都是经济和社会上重要的牲畜物种，用于运输和生产牛奶和肉类。就像牛和马一样，骆驼可以在工业化农业条件下发现，也可以用于体育运动。骆驼比赛是一个价值数百万美元的产业，一些标本的价值超过950万美元。尽管单峰骆驼对人类有明显的价值，但它在基因组学中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，但骆驼只组装到支架水平，这并没有明确指示测序片段的顺序或染色体位置。在这项研究中，参考辅助染色体组装（RACA）算法被实现，以使用骆驼支架的读对信息，与牛和人类基因组对齐，以便在近染色体水平组装中组织和定向这些支架。该方法产生了72个大尺寸片段（N50 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，使我们能够进一步升级组装。这单峰骆驼组装将是一个宝贵的工具，以验证未来的骆驼组装产生的染色质构象或/和长读技术。这项研究提供了单峰骆驼的第一个近染色体组装，从而将这个经济上重要的物种添加到关于驯养牲畜基因组结构的知识库中。
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.