author_facet Bai, Chang-Ming
Xin, Lu-Sheng
Rosani, Umberto
Wu, Biao
Wang, Qing-Chen
Duan, Xiao-Ke
Liu, Zhi-Hong
Wang, Chong-Ming
Bai, Chang-Ming
Xin, Lu-Sheng
Rosani, Umberto
Wu, Biao
Wang, Qing-Chen
Duan, Xiao-Ke
Liu, Zhi-Hong
Wang, Chong-Ming
author Bai, Chang-Ming
Xin, Lu-Sheng
Rosani, Umberto
Wu, Biao
Wang, Qing-Chen
Duan, Xiao-Ke
Liu, Zhi-Hong
Wang, Chong-Ming
spellingShingle Bai, Chang-Ming
Xin, Lu-Sheng
Rosani, Umberto
Wu, Biao
Wang, Qing-Chen
Duan, Xiao-Ke
Liu, Zhi-Hong
Wang, Chong-Ming
GigaScience
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
Computer Science Applications
Health Informatics
author_sort bai, chang-ming
spelling Bai, Chang-Ming Xin, Lu-Sheng Rosani, Umberto Wu, Biao Wang, Qing-Chen Duan, Xiao-Ke Liu, Zhi-Hong Wang, Chong-Ming 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giz067 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.</jats:p> </jats:sec> Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C GigaScience
doi_str_mv 10.1093/gigascience/giz067
facet_avail Online
Free
finc_class_facet Informatik
Medizin
format ElectronicArticle
fullrecord blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9naWdhc2NpZW5jZS9naXowNjc
id ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9naWdhc2NpZW5jZS9naXowNjc
institution DE-Zwi2
DE-D161
DE-Gla1
DE-Zi4
DE-15
DE-Rs1
DE-Pl11
DE-105
DE-14
DE-Ch1
DE-L229
DE-D275
DE-Bn3
DE-Brt1
imprint Oxford University Press (OUP), 2019
imprint_str_mv Oxford University Press (OUP), 2019
issn 2047-217X
issn_str_mv 2047-217X
language English
mega_collection Oxford University Press (OUP) (CrossRef)
match_str bai2019chromosomallevelassemblyofthebloodclamscapharcaanadarabroughtoniiusinglongsequencereadsandhic
publishDateSort 2019
publisher Oxford University Press (OUP)
recordtype ai
record_format ai
series GigaScience
source_id 49
title Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_unstemmed Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_full Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_fullStr Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_full_unstemmed Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_short Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_sort chromosomal-level assembly of the blood clam, scapharca (anadara) broughtonii, using long sequence reads and hi-c
topic Computer Science Applications
Health Informatics
url http://dx.doi.org/10.1093/gigascience/giz067
publishDate 2019
physical
description <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.</jats:p> </jats:sec>
container_issue 7
container_start_page 0
container_title GigaScience
container_volume 8
format_de105 Article, E-Article
format_de14 Article, E-Article
format_de15 Article, E-Article
format_de520 Article, E-Article
format_de540 Article, E-Article
format_dech1 Article, E-Article
format_ded117 Article, E-Article
format_degla1 E-Article
format_del152 Buch
format_del189 Article, E-Article
format_dezi4 Article
format_dezwi2 Article, E-Article
format_finc Article, E-Article
format_nrw Article, E-Article
_version_ 1792346315901894666
geogr_code not assigned
last_indexed 2024-03-01T17:37:27.336Z
geogr_code_person not assigned
openURL url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Chromosomal-level+assembly+of+the+blood+clam%2C+Scapharca+%28Anadara%29+broughtonii%2C+using+long+sequence+reads+and+Hi-C&rft.date=2019-07-01&genre=article&issn=2047-217X&volume=8&issue=7&jtitle=GigaScience&atitle=Chromosomal-level+assembly+of+the+blood+clam%2C+Scapharca+%28Anadara%29+broughtonii%2C+using+long+sequence+reads+and+Hi-C&aulast=Wang&aufirst=Chong-Ming&rft_id=info%3Adoi%2F10.1093%2Fgigascience%2Fgiz067&rft.language%5B0%5D=eng
SOLR
_version_ 1792346315901894666
author Bai, Chang-Ming, Xin, Lu-Sheng, Rosani, Umberto, Wu, Biao, Wang, Qing-Chen, Duan, Xiao-Ke, Liu, Zhi-Hong, Wang, Chong-Ming
author_facet Bai, Chang-Ming, Xin, Lu-Sheng, Rosani, Umberto, Wu, Biao, Wang, Qing-Chen, Duan, Xiao-Ke, Liu, Zhi-Hong, Wang, Chong-Ming, Bai, Chang-Ming, Xin, Lu-Sheng, Rosani, Umberto, Wu, Biao, Wang, Qing-Chen, Duan, Xiao-Ke, Liu, Zhi-Hong, Wang, Chong-Ming
author_sort bai, chang-ming
container_issue 7
container_start_page 0
container_title GigaScience
container_volume 8
description <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.</jats:p> </jats:sec>
doi_str_mv 10.1093/gigascience/giz067
facet_avail Online, Free
finc_class_facet Informatik, Medizin
format ElectronicArticle
format_de105 Article, E-Article
format_de14 Article, E-Article
format_de15 Article, E-Article
format_de520 Article, E-Article
format_de540 Article, E-Article
format_dech1 Article, E-Article
format_ded117 Article, E-Article
format_degla1 E-Article
format_del152 Buch
format_del189 Article, E-Article
format_dezi4 Article
format_dezwi2 Article, E-Article
format_finc Article, E-Article
format_nrw Article, E-Article
geogr_code not assigned
geogr_code_person not assigned
id ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9naWdhc2NpZW5jZS9naXowNjc
imprint Oxford University Press (OUP), 2019
imprint_str_mv Oxford University Press (OUP), 2019
institution DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Rs1, DE-Pl11, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1
issn 2047-217X
issn_str_mv 2047-217X
language English
last_indexed 2024-03-01T17:37:27.336Z
match_str bai2019chromosomallevelassemblyofthebloodclamscapharcaanadarabroughtoniiusinglongsequencereadsandhic
mega_collection Oxford University Press (OUP) (CrossRef)
physical
publishDate 2019
publishDateSort 2019
publisher Oxford University Press (OUP)
record_format ai
recordtype ai
series GigaScience
source_id 49
spelling Bai, Chang-Ming Xin, Lu-Sheng Rosani, Umberto Wu, Biao Wang, Qing-Chen Duan, Xiao-Ke Liu, Zhi-Hong Wang, Chong-Ming 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giz067 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.</jats:p> </jats:sec> Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C GigaScience
spellingShingle Bai, Chang-Ming, Xin, Lu-Sheng, Rosani, Umberto, Wu, Biao, Wang, Qing-Chen, Duan, Xiao-Ke, Liu, Zhi-Hong, Wang, Chong-Ming, GigaScience, Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C, Computer Science Applications, Health Informatics
title Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_full Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_fullStr Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_full_unstemmed Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_short Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
title_sort chromosomal-level assembly of the blood clam, scapharca (anadara) broughtonii, using long sequence reads and hi-c
title_unstemmed Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
topic Computer Science Applications, Health Informatics
url http://dx.doi.org/10.1093/gigascience/giz067