Chao Yang1,2, Xuejuan Li1, Qingxiong Wang2, Hao Yuan1, Yuan Huang3, Hong Xiao4. 1. College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China. 2. Shaanxi Institute of Zoology, Xi'an, 710032, China. 3. College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China. yuanh@snnu.edu.cn. 4. Shaanxi Institute of Zoology, Xi'an, 710032, China. xh4500@163.com.
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.
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.
Entities:
Keywords:
Habitat loss; Larus relictus; PacBio sequencing; Population fragmentation; Whole-genome
Authors: Francesca Giordano; Louise Aigrain; Michael A Quail; Paul Coupland; James K Bonfield; Robert M Davies; German Tischler; David K Jackson; Thomas M Keane; Jing Li; Jia-Xing Yue; Gianni Liti; Richard Durbin; Zemin Ning Journal: Sci Rep Date: 2017-06-21 Impact factor: 4.379
Authors: Shaohong Feng; Josefin Stiller; Yuan Deng; Joel Armstrong; Qi Fang; Andrew Hart Reeve; Duo Xie; Guangji Chen; Chunxue Guo; Brant C Faircloth; Bent Petersen; Zongji Wang; Qi Zhou; Mark Diekhans; Wanjun Chen; Sergio Andreu-Sánchez; Ashot Margaryan; Jason Travis Howard; Carole Parent; George Pacheco; Mikkel-Holger S Sinding; Lara Puetz; Emily Cavill; Ângela M Ribeiro; Leopold Eckhart; Jon Fjeldså; Peter A Hosner; Robb T Brumfield; Les Christidis; Mads F Bertelsen; Thomas Sicheritz-Ponten; Dieter Thomas Tietze; Bruce C Robertson; Gang Song; Gerald Borgia; Santiago Claramunt; Irby J Lovette; Saul J Cowen; Peter Njoroge; John Philip Dumbacher; Oliver A Ryder; Jérôme Fuchs; Michael Bunce; David W Burt; Joel Cracraft; Guanliang Meng; Shannon J Hackett; Peter G Ryan; Knud Andreas Jønsson; Ian G Jamieson; Rute R da Fonseca; Edward L Braun; Peter Houde; Siavash Mirarab; Alexander Suh; Bengt Hansson; Suvi Ponnikas; Hanna Sigeman; Martin Stervander; Paul B Frandsen; Henriette van der Zwan; Rencia van der Sluis; Carina Visser; Christopher N Balakrishnan; Andrew G Clark; John W Fitzpatrick; Reed Bowman; Nancy Chen; Alison Cloutier; Timothy B Sackton; Scott V Edwards; Dustin J Foote; Subir B Shakya; Frederick H Sheldon; Alain Vignal; André E R Soares; Beth Shapiro; Jacob González-Solís; Joan Ferrer-Obiol; Julio Rozas; Marta Riutort; Anna Tigano; Vicki Friesen; Love Dalén; Araxi O Urrutia; Tamás Székely; Yang Liu; Michael G Campana; André Corvelo; Robert C Fleischer; Kim M Rutherford; Neil J Gemmell; Nicolas Dussex; Henrik Mouritsen; Nadine Thiele; Kira Delmore; Miriam Liedvogel; Andre Franke; Marc P Hoeppner; Oliver Krone; Adam M Fudickar; Borja Milá; Ellen D Ketterson; Andrew Eric Fidler; Guillermo Friis; Ángela M Parody-Merino; Phil F Battley; Murray P Cox; Nicholas Costa Barroso Lima; Francisco Prosdocimi; Thomas Lee Parchman; Barney A Schlinger; Bette A Loiselle; John G Blake; Haw Chuan Lim; Lainy B Day; Matthew J Fuxjager; Maude W Baldwin; Michael J Braun; Morgan Wirthlin; Rebecca B Dikow; T Brandt Ryder; Glauco Camenisch; Lukas F Keller; Jeffrey M DaCosta; Mark E Hauber; Matthew I M Louder; Christopher C Witt; Jimmy A McGuire; Joann Mudge; Libby C Megna; Matthew D Carling; Biao Wang; Scott A Taylor; Glaucia Del-Rio; Alexandre Aleixo; Ana Tereza Ribeiro Vasconcelos; Claudio V Mello; Jason T Weir; David Haussler; Qiye Li; Huanming Yang; Jian Wang; Fumin Lei; Carsten Rahbek; M Thomas P Gilbert; Gary R Graves; Erich D Jarvis; Benedict Paten; Guojie Zhang Journal: Nature Date: 2020-11-11 Impact factor: 49.962