title: Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.
abstract: The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis Consortium. The draft was based on whole-genome shotgun sequencing, and the current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions and supercontigs and relatively short contigs that are unmapped to chromosomes in the draft genome. We performed resequencing and assembly of the genome of common marmoset by deep sequencing with high-throughput sequencing technology. Several different sequence runs using Illumina sequencing platforms were executed, and 181 Gbp of high-quality bases including mate-pairs with long insert lengths of 3, 8, 20, and 40 Kbp were obtained, that is, approximately 60× coverage. The resequencing significantly improved the MGSAC draft genome sequence. The N50 of the contigs, which is a statistical measure used to evaluate assembly quality, doubled. As a result, 51% of the contigs (total length: 299 Mbp) that were unmapped to chromosomes in the MGSAC draft were merged with chromosomal contigs, and the improved genome sequence helped to detect 5,288 new genes that are homologous to human cDNAs and the gaps in 5,187 transcripts of the Ensembl gene annotations were completely filled.
authors.affiliation: Department of Biosciences and Informatics, Keio University, Japan.
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
authors.affiliation: Department of Genome Medicine, National Research Institute for Child Health and Development, NCCHD, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.affiliation: Department of Applied Developmental Biology, Central Institute for Experimental Animals, Japan.
authors.forename: Wakako
authors.initials: W
authors.lastname: Kumita
authors.affiliation: Principles of Informatics Research Division, National Institute of Informatics, Japan.|Center for Information Biology, National Institute of Genetics, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: Center for Information Biology, National Institute of Genetics, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Preventive Medicine and Diagnosis Innovation Program, RIEKN, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.affiliation: Laboratory for Symbolic Cognitive Development, Brain Science Institute RIKEN, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Iriki
authors.affiliation: Department of Applied Developmental Biology, Central Institute for Experimental Animals, Japan.|Keio Advanced Research Center, Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Sasaki
authors.affiliation: Department of Physiology, Keio University School of Medicine, Japan.|Laboratory for Marmoset Neural Architecture, RIKEN Brain Science Institute.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Okano
authors.affiliation: Department of Biosciences and Informatics, Keio University, Japan.
authors.forename: Yasubumi
authors.initials: Y
authors.lastname: Sakakibara
mesh_terms: D000818:Animals; D002144:Callithrix; D020451:Contig Mapping / Q000379:methods; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods; D016366:Open Reading Frames / Q000235:genetics*; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA / Q000379:methods*