Dataset Information

A High-Quality Draft Genome Assembly of the Black-Necked Crane (Grus nigricollis) Based on Nanopore Sequencing.

ABSTRACT: The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world's 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59?Gb Illumina short reads and 116.5?Gb nanopore long reads were generated. The 1.23?Gb assembled genome has a high contig N50 of 17.89?Mb, and has a longest contig of 87.83?Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat.

SUBMITTER: Zhou C

PROVIDER: S-EPMC7145580 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Publications

A High-Quality Draft Genome Assembly of the Black-Necked Crane (Grus nigricollis) Based on Nanopore Sequencing.

Zhou Chuang C Yu Haoran H Geng Yang Y Liu Wei W Zheng Shuai S Yang Nan N Meng Yang Y Dou Liang L Price Megan M Ran Jianghong J Yue Bisong B Wu Yongjie Y

Genome biology and evolution 20191201 12

The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world's 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a lo ...[more]

PMID: 31725151

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Project description:BackgroundThe black-necked crane (Grus nigricollis) is a vulnerable species and the only species that lives in the plateau. Five migration routes of different populations have been identified, but for cranes wintering in Nyingchi Prefecture, Tibet, the migration route and breeding/summering area are still unknown. The aim of this study was to investigate the spatio-temporal migration patterns of black-necked cranes in this area and to identify important areas for conservation.MethodsIn 2016, we fitted seven black-necked cranes in Nyingchi with GPS-GSM satellite transmitters to record their migration routes. We used ArcGIS 10.2 to visualize important stopover sites and the 'ggplot' function in R to analyze the migration patterns.ResultsFrom March 2016 to May 2019, we recorded nine spring migration and four autumn migration tracks from five individuals. Four individuals spent the breeding/summering season in Qinghai Lake, while the other spent the breeding/summering season in the Jinzihai Wetland of Dulan County, Qinghai Province. Detailed spatio-temporal information showed that the spring migration lasted 8.7 ± 4.6 days and covered 1,182.5 ± 90.4 km, while the autumn migration lasted 30 ± 10.6 days and covered 1,455.7 ± 138 km. Basom Lake and the Shazhuyu River were the most important stopover sites during the spring and autumn migrations, respectively. The cranes spent 4.4 ± 3.7 days in Basom Lake and 26.3 ± 10.7 days in the Shazhuyu River. The black-necked cranes mainly migrated during the daytime (>85 % of the fly points), and 81 % (17/21) of all stopover and roosting sites were in the valley or at lakeside swamps. Only 17.7% (516 / 2,914) of the data points for stopover and roosting sites were in protected areas.Main conclusionsOur study revealed the breeding/summering areas and migration routes of the black-necked cranes wintering in Nyingchi. These results contribute to a better understanding of the annual spatio-temporal migration patterns and the development of conservation plans for this vulnerable species.

Dataset Information

A High-Quality Draft Genome Assembly of the Black-Necked Crane (Grus nigricollis) Based on Nanopore Sequencing.

Publications

A High-Quality Draft Genome Assembly of the Black-Necked Crane (Grus nigricollis) Based on Nanopore Sequencing.

Similar Datasets

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