An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
Abstract Background The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcrip...
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doaj-af2b7422648a4770aa14a92dcd6881e52020-11-25T03:23:02ZengBMCBMC Genomics1471-21642020-04-0121S31910.1186/s12864-020-6657-2An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence dataVasanthan Jayakumar0Hiromi Ishii1Misato Seki2Wakako Kumita3Takashi Inoue4Sumitaka Hase5Kengo Sato6Hideyuki Okano7Erika Sasaki8Yasubumi Sakakibara9Department of Biosciences and Informatics, Keio UniversityDepartment of Biosciences and Informatics, Keio UniversityDepartment of Biosciences and Informatics, Keio UniversityDepartment of Marmoset Biology and Medicine, Central Institute for Experimental AnimalsDepartment of Marmoset Biology and Medicine, Central Institute for Experimental AnimalsDepartment of Biosciences and Informatics, Keio UniversityDepartment of Biosciences and Informatics, Keio UniversityDepartment of Physiology, Keio University School of MedicineDepartment of Marmoset Biology and Medicine, Central Institute for Experimental AnimalsDepartment of Biosciences and Informatics, Keio UniversityAbstract Background The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. Results Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. Conclusions Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.http://link.springer.com/article/10.1186/s12864-020-6657-2Common marmosetCallithrix jacchusDe novo assemblyNon-human primate genomicsChromosome-scale scaffolds |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Vasanthan Jayakumar Hiromi Ishii Misato Seki Wakako Kumita Takashi Inoue Sumitaka Hase Kengo Sato Hideyuki Okano Erika Sasaki Yasubumi Sakakibara |
spellingShingle |
Vasanthan Jayakumar Hiromi Ishii Misato Seki Wakako Kumita Takashi Inoue Sumitaka Hase Kengo Sato Hideyuki Okano Erika Sasaki Yasubumi Sakakibara An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data BMC Genomics Common marmoset Callithrix jacchus De novo assembly Non-human primate genomics Chromosome-scale scaffolds |
author_facet |
Vasanthan Jayakumar Hiromi Ishii Misato Seki Wakako Kumita Takashi Inoue Sumitaka Hase Kengo Sato Hideyuki Okano Erika Sasaki Yasubumi Sakakibara |
author_sort |
Vasanthan Jayakumar |
title |
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
title_short |
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
title_full |
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
title_fullStr |
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
title_full_unstemmed |
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
title_sort |
improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-04-01 |
description |
Abstract Background The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. Results Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. Conclusions Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data. |
topic |
Common marmoset Callithrix jacchus De novo assembly Non-human primate genomics Chromosome-scale scaffolds |
url |
http://link.springer.com/article/10.1186/s12864-020-6657-2 |
work_keys_str_mv |
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