古巴鳄基因组草图的组装与注释。
Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome.
机构信息
Department of Biology, Montclair State University, Montclair, NJ, USA.
Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
出版信息
BMC Genom Data. 2024 Jun 6;25(1):53. doi: 10.1186/s12863-024-01240-y.
OBJECTIVES
The new data provide an important genomic resource for the Critically Endangered Cuban crocodile (Crocodylus rhombifer). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile (Crocodylus acutus) in areas of sympatry. The reported de novo assembly will contribute to studies of crocodylian evolutionary history and provide a resource for informing Cuban crocodile conservation.
DATA DESCRIPTION
The final 2.2 Gb draft genome for C. rhombifer consists of 41,387 scaffolds (contigs: N50 = 104.67 Kb; scaffold: N50-518.55 Kb). Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 92.3% of the 3,354 genes in the vertebrata_odb10 database. Approximately 42% of the genome (960Mbp) comprises repeat elements. We predicted 30,138 unique protein-coding sequences (17,737 unique genes) in the genome assembly. Functional annotation found the top Gene Ontology annotations for Biological Processes, Molecular Function, and Cellular Component were regulation, protein, and intracellular, respectively. This assembly will support future macroevolutionary, conservation, and molecular studies of the Cuban crocodile.
目的
新数据为极度濒危的古巴鳄（Crocodylus rhombifer）提供了重要的基因组资源。古巴鳄仅分布在古巴南部马坦萨斯省的萨帕塔沼泽，与广泛分布的美洲鳄（Crocodylus acutus）在同域地区容易杂交。报告的从头组装将有助于研究鳄鱼的进化历史，并为保护古巴鳄提供资源。
数据描述
C. rhombifer 的最终 22 亿碱基对的草图基因组由 41387 个支架（重叠群：N50=104.67 Kb；支架：N50-518.55 Kb）组成。通用单拷贝同源基因（BUSCO）基准测试鉴定出脊椎动物_odb10 数据库中 3354 个基因中的 92.3%。基因组的大约 42%（960Mbp）由重复元件组成。我们在基因组组装中预测了 30138 个独特的蛋白质编码序列（17737 个独特基因）。功能注释发现，生物过程、分子功能和细胞成分的顶级基因本体论注释分别是调节、蛋白质和细胞内。该组装将支持未来对古巴鳄的宏观进化、保护和分子研究。
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