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. 2021 Apr 29;22(1):311.
doi: 10.1186/s12864-021-07616-z.

Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications

Chao Yang #  1   2 , Xuejuan Li #  1 , Qingxiong Wang  2 , Hao Yuan  1 , Yuan Huang  3 , Hong Xiao  4
Affiliations

Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications

Chao Yang et al. BMC Genomics. .

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Keywords: Habitat loss; Larus relictus; PacBio sequencing; Population fragmentation; Whole-genome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Topology of Maximum likelihood (ML) tree for 12 Charadriiformes species. Tree reconstruction based on single-copy orthologues protein sequences under IQ-TREE v1.6.11. BioSample numbers are indicated following species name. Numbers on nodes are bootstrap values
Fig. 2
Fig. 2
Timing of inferred divergence of 12 Charadriiformes species. Numbers on the nodes represent divergence times supported by 95% HPD
Fig. 3
Fig. 3
The PSMC analyses result of Larus relictus. An individual re-sequencing raw data was obtained in NCBI with accession number SRR14041273. One hundred iterations were performed
See this image and copyright information in PMC

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