Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian
The southern giant petrel Macronectes giganteus , a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarct...
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ftdoajarticles:oai:doaj.org/article:128768936d734f618f95565eedea141a 2023-05-15T13:41:59+02:00 Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian Sun-Hee Kim Seung-Jae Lee Euna Jo Jangyeon Kim Jong-U Kim Jeong-Hoon Kim Hyun Park Young-Min Chi 2021-07-01T00:00:00Z https://doi.org/10.3390/ani11072046 https://doaj.org/article/128768936d734f618f95565eedea141a EN eng MDPI AG https://www.mdpi.com/2076-2615/11/7/2046 https://doaj.org/toc/2076-2615 doi:10.3390/ani11072046 2076-2615 https://doaj.org/article/128768936d734f618f95565eedea141a Animals, Vol 11, Iss 2046, p 2046 (2021) southern giant petrel Macronectes giganteus genome assembly annotation PacBio sequencing 10x Genomics Chromium technology Veterinary medicine SF600-1100 Zoology QL1-991 article 2021 ftdoajarticles https://doi.org/10.3390/ani11072046 2022-12-31T06:23:56Z The southern giant petrel Macronectes giganteus , a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarctic and sub-Antarctic regions, studies on the status of some populations and the associated genetic data are currently extremely limited. In this study, we assembled the genome of M. giganteus by integrating Pacific Biosciences single-molecule real-time sequencing and the Chromium system developed by 10x Genomics. The final M. giganteus genome assembly was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb. The M. giganteus genome contains 14,993 predicted protein-coding genes and has 11.06% repeat sequences. Estimated historical effective population size analysis indicated that the southern giant petrel underwent a severe reduction in effective population size during a period coinciding with the early Pleistocene. The availability of this newly sequenced genome will facilitate more effective genetic monitoring of threatened species. Furthermore, the genome will provide a valuable resource for gene functional studies and further comparative genomic studies on the life history and ecological traits of specific avian species. Article in Journal/Newspaper Antarc* Antarctic Giant Petrel Macronectes giganteus Directory of Open Access Journals: DOAJ Articles Antarctic The Antarctic Pacific Giganteus ENVELOPE(62.500,62.500,-67.567,-67.567) Animals 11 7 2046 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
southern giant petrel Macronectes giganteus genome assembly annotation PacBio sequencing 10x Genomics Chromium technology Veterinary medicine SF600-1100 Zoology QL1-991 |
spellingShingle |
southern giant petrel Macronectes giganteus genome assembly annotation PacBio sequencing 10x Genomics Chromium technology Veterinary medicine SF600-1100 Zoology QL1-991 Sun-Hee Kim Seung-Jae Lee Euna Jo Jangyeon Kim Jong-U Kim Jeong-Hoon Kim Hyun Park Young-Min Chi Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
topic_facet |
southern giant petrel Macronectes giganteus genome assembly annotation PacBio sequencing 10x Genomics Chromium technology Veterinary medicine SF600-1100 Zoology QL1-991 |
description |
The southern giant petrel Macronectes giganteus , a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarctic and sub-Antarctic regions, studies on the status of some populations and the associated genetic data are currently extremely limited. In this study, we assembled the genome of M. giganteus by integrating Pacific Biosciences single-molecule real-time sequencing and the Chromium system developed by 10x Genomics. The final M. giganteus genome assembly was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb. The M. giganteus genome contains 14,993 predicted protein-coding genes and has 11.06% repeat sequences. Estimated historical effective population size analysis indicated that the southern giant petrel underwent a severe reduction in effective population size during a period coinciding with the early Pleistocene. The availability of this newly sequenced genome will facilitate more effective genetic monitoring of threatened species. Furthermore, the genome will provide a valuable resource for gene functional studies and further comparative genomic studies on the life history and ecological traits of specific avian species. |
format |
Article in Journal/Newspaper |
author |
Sun-Hee Kim Seung-Jae Lee Euna Jo Jangyeon Kim Jong-U Kim Jeong-Hoon Kim Hyun Park Young-Min Chi |
author_facet |
Sun-Hee Kim Seung-Jae Lee Euna Jo Jangyeon Kim Jong-U Kim Jeong-Hoon Kim Hyun Park Young-Min Chi |
author_sort |
Sun-Hee Kim |
title |
Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
title_short |
Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
title_full |
Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
title_fullStr |
Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
title_full_unstemmed |
Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian |
title_sort |
genome of the southern giant petrel assembled using third-generation dna sequencing and linked reads reveals evolutionary traits of southern avian |
publisher |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/ani11072046 https://doaj.org/article/128768936d734f618f95565eedea141a |
long_lat |
ENVELOPE(62.500,62.500,-67.567,-67.567) |
geographic |
Antarctic The Antarctic Pacific Giganteus |
geographic_facet |
Antarctic The Antarctic Pacific Giganteus |
genre |
Antarc* Antarctic Giant Petrel Macronectes giganteus |
genre_facet |
Antarc* Antarctic Giant Petrel Macronectes giganteus |
op_source |
Animals, Vol 11, Iss 2046, p 2046 (2021) |
op_relation |
https://www.mdpi.com/2076-2615/11/7/2046 https://doaj.org/toc/2076-2615 doi:10.3390/ani11072046 2076-2615 https://doaj.org/article/128768936d734f618f95565eedea141a |
op_doi |
https://doi.org/10.3390/ani11072046 |
container_title |
Animals |
container_volume |
11 |
container_issue |
7 |
container_start_page |
2046 |
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1766161678457634816 |