Dataset Information

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.

SUBMITTER: Sato K

PROVIDER: S-EPMC4653617 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

Sato Kengo K Kuroki Yoko Y Kumita Wakako W Fujiyama Asao A Toyoda Atsushi A Kawai Jun J Iriki Atsushi A Sasaki Erika E Okano Hideyuki H Sakakibara Yasubumi Y

Scientific reports 20151120

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 sequenc ...[more]

PMID: 26586576

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Project description:Facial expressions are subtle cues, central for communication and conveying emotions in mammals. Traditionally, facial expressions have been classified as a whole (e.g. happy, angry, bared-teeth), due to automatic face processing in the human brain, i.e., humans categorise emotions globally, but are not aware of subtle or isolated cues such as an eyebrow raise. Moreover, the same facial configuration (e.g. lip corners pulled backwards exposing teeth) can convey widely different information depending on the species (e.g. humans: happiness; chimpanzees: fear). The Facial Action Coding System (FACS) is considered the gold standard for investigating human facial behaviour and avoids subjective interpretations of meaning by objectively measuring independent movements linked to facial muscles, called Action Units (AUs). Following a similar methodology, we developed the CalliFACS for the common marmoset. First, we determined the facial muscular plan of the common marmoset by examining dissections from the literature. Second, we recorded common marmosets in a variety of contexts (e.g. grooming, feeding, play, human interaction, veterinary procedures), and selected clips from online databases (e.g. YouTube) to identify their facial movements. Individual facial movements were classified according to appearance changes produced by the corresponding underlying musculature. A diverse repertoire of 33 facial movements was identified in the common marmoset (15 Action Units, 15 Action Descriptors and 3 Ear Action Descriptors). Although we observed a reduced range of facial movement when compared to the HumanFACS, the common marmoset's range of facial movements was larger than predicted according to their socio-ecology and facial morphology, which indicates their importance for social interactions. CalliFACS is a scientific tool to measure facial movements, and thus, allows us to better understand the common marmoset's expressions and communication. As common marmosets have become increasingly popular laboratory animal models, from neuroscience to cognition, CalliFACS can be used as an important tool to evaluate their welfare, particularly in captivity.

Dataset Information

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

Publications

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

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