Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

Abstract

BackgroundThe relict gull (Larus relictus), one of the least known Aves, 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.ResultsIn this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, the first reference genome of the 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 protein-coding 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. The phylogenetic tree was constructed using 7,339 single-copy orthologous genes, which showed Charadriiformes located at the basal position and Philomachus pugnax as the closest relative of L. relictus. The divergence time between L. relictus and P. pugnax was ~68.44 Mya. The population dynamics of the Ordos breeding subpopulation in Hongjian Nur is a good confirmation that these birds are suffering from habitat loss and fragmentation.ConclusionsThis assembled genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and helps to establish a foundation for further studies investigating whether the other three breeding subpopulations have combined with the Ordos breeding subpopulation. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to improve the fragmentation of breeding populations.

A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high‐altitude adaptation

“…For PacBio long read sequencing, G-TUBE was used to shear the genomic DNA. The detailed sequencing steps were consistent with our previous studies (Li et al 2021;Yang et al 2021).…”