Yang Chao, Li Xuejuan, Wang Qingxiong, Yuan Hao, Huang Yuan, Xiao Hong
College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
Shaanxi Institute of Zoology, Xi'an, 710032, China.
BMC Genomics. 2021 Apr 29;22(1):311. doi: 10.1186/s12864-021-07616-z.
The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation.
In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals.
This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations.
遗鸥（Larus relictus）在国际自然保护联盟（IUCN）红色名录中被列为易危物种，在中国是国家一级保护鸟类。目前缺乏遗鸥的基因组资源，这限制了对其进化和保护的研究。
在本研究中，基于Illumina和PacBio测序平台，我们成功组装了遗鸥的基因组，这是鸥属中少数已知的参考基因组之一。最终组装的基因组大小为1.21 Gb，重叠群N50为8.11 Mb。从组装结果中预测出总共18454个基因，其中16967个（91.94%）基因得到注释。该基因组包含92.52 Mb的重复序列，占组装序列的7.63%。使用4902个单拷贝直系同源基因构建了系统发育树，结果显示遗鸥与史氏鸥（L. smithsonianus）亲缘关系最近，估计它们之间的分歧时间为1470万年前。PSMC分析表明，遗鸥在0.01 - 0.1百万年前经历了长期的种群数量下降，有效种群大小从8800个个体减少到2200个个体。
该基因组将为遗鸥的一系列基因组和保护研究提供宝贵的基因组资源，并有助于为进一步研究繁殖种群是否为复合种群奠定基础。由于该物种受到栖息地丧失和破碎化的威胁，建议采取行动保护遗鸥，以缓解繁殖种群碎片化的问题。
