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

Published on Dec 1, 2015in Scientific Reports4.011
· DOI :10.1038/srep16894
Kengo Sato18
Estimated H-index: 18
Yoko Kuroki18
Estimated H-index: 18
+ 7 AuthorsYasubumi Sakakibara29
Estimated H-index: 29
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.
  • References (26)
  • Citations (14)
📖 Papers frequently viewed together
23 Authors (Erika Sasaki, ..., Tatsuji Nomura)
453 Citations
219 Citations
123 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#1Hideyuki Okano (Keio: Keio University)H-Index: 112
#2Atsushi MiyawakiH-Index: 52
Last. Kiyoto Kasai (UTokyo: University of Tokyo)H-Index: 54
view all 3 authors...
There is an emerging interest in brain-mapping projects in countries across the world, including the USA, Europe, Australia and China. In 2014, Japan started a brain-mapping project called Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS). Brain/MINDS aims to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain, and takes advantage of a unique non-human primate animal model, the common marmoset ( Callith...
40 CitationsSource
#1Juan Carlos Izpisua Belmonte (Salk Institute for Biological Studies)H-Index: 84
#2Edward M. Callaway (Salk Institute for Biological Studies)H-Index: 66
Last. Feng ZhangH-Index: 115
view all 21 authors...
One of the great strengths of the mouse model is the wide array of genetic tools that have been developed. Striking examples include methods for directed modification of the genome, and for regulated expression or inactivation of genes. Within neuroscience, it is now routine to express reporter genes, neuronal activity indicators, and opsins in specific neuronal types in the mouse. However, there are considerable anatomical, physiological, cognitive, and behavioral differences between the mouse ...
124 CitationsSource
#1Hideyuki Okano (Keio: Keio University)H-Index: 112
#2Partha P. Mitra (CSHL: Cold Spring Harbor Laboratory)H-Index: 53
Globally, there is an increasing interest in brain-mapping projects, including the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative project in the USA, the Human Brain Project (HBP) in Europe, and the Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) project in Japan. These projects aim to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain. Brain/MINDS is focused on stru...
53 CitationsSource
#1Noriyuki Kishi (Keio: Keio University)H-Index: 11
#2Kenya Sato (Central Institute for Experimental Animals)H-Index: 3
Last. Hideyuki Okano (Keio: Keio University)H-Index: 112
view all 4 authors...
The common marmoset (Callithrix jacchus) is a small New World primate; it originally comes from the Atlantic coastal forests in northeastern Brazil. It has been attracting much attention in the biomedical research field because of its size, availability, and unique biological characteristics. Its endocrinological and behavioral similarity to humans, comparative ease in handling, and high reproductive efficiency are very advantageous for neuroscience research. Recently, we developed transgenic co...
99 CitationsSource
#1Kim C. Worley (BCM: Baylor College of Medicine)H-Index: 57
#2Wesley C. WarrenH-Index: 57
Last. Richard K. WilsonH-Index: 156
view all 111 authors...
Kim Worley and colleagues report the whole-genome sequence of the common marmoset, Callithrix jacchus, the first New World monkey to be sequenced.
131 CitationsSource
#1Sebastiaan van Heesch (UU: Utrecht University)H-Index: 16
Last. Edwin Cuppen (UU: Utrecht University)H-Index: 67
view all 12 authors...
Background: Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. Results: Here, we systematically assessed the utility of paired-end and mate-pair (MP) next-generation sequencing libraries with insert sizes ranging from 170 bp to 25 kb, for genome coverage and for improving scaffolding of a mammalian genome (Rattus no...
22 CitationsSource
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners t...
1,902 CitationsSource
#1Le Cong (MIT: Massachusetts Institute of Technology)H-Index: 16
#2F. Ann Ran (MIT: Massachusetts Institute of Technology)H-Index: 10
Last. Feng Zhang (MIT: Massachusetts Institute of Technology)H-Index: 115
view all 11 authors...
Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9...
6,987 CitationsSource
#1Prashant Mali (Harvard University)H-Index: 31
#2Luhan Yang (Harvard University)H-Index: 16
Last. George M Church G M (Wyss Institute for Biologically Inspired Engineering)H-Index: 142
view all 8 authors...
Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cel...
4,913 CitationsSource
#1Lenore Pipes (UW: University of Washington)H-Index: 4
#2Sheng Li (UW: University of Washington)H-Index: 14
Last. Michael G. Katze (UW: University of Washington)H-Index: 84
view all 15 authors...
RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality. However, uniform resources for raw, cleaned and processed RNA-Seq data are sparse for most organisms and this is especially true fo...
45 CitationsSource
Cited By14
#1Marina Brasó-Vives (UPF: Pompeu Fabra University)
#2Inna S. Povolotskaya (RSMU: Russian National Research Medical University)H-Index: 9
Last. Arcadi NavarroH-Index: 33
view all 13 authors...
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research ...
#1Vasanthan Jayakumar (Keio: Keio University)H-Index: 2
#2Hiromi Ishii (Keio: Keio University)
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 10 authors...
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 G...
#1Shotaro Uehara (Showa Pharmaceutical University)H-Index: 16
#2Yasuhiro Uno (Kadai: Kagoshima University)H-Index: 20
Last. Hiroshi Yamazaki (Showa Pharmaceutical University)H-Index: 68
view all 3 authors...
Abstract The common marmoset (Callithrix jacchus) is a New World monkey that has attracted much attention as a potentially useful primate model for preclinical testing. A total of 36 marmoset cytochrome P450 (P450) isoforms in the P450 1–51 subfamilies have been identified and characterized by the application of genome analysis and molecular functional characterization. In this mini-review, we provide an overview of the genomic structures, sequence identities, and substrate selectivities of marm...
#1Wakako Kumita (Central Institute for Experimental Animals)H-Index: 2
#2Kenya Sato (Central Institute for Experimental Animals)H-Index: 3
Last. Erika Sasaki (Central Institute for Experimental Animals)H-Index: 21
view all 13 authors...
Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled production of target-gene knock-out (KO) NHP models. Target-gene-KO/knock-in (KI) efficiency of CRISPR/Cas9 has not been extensively investigated in marmosets. In this study, optimum conditions for target gene modification efficacies of CRISPR/mRNA and CRISPR/nuclease in marmoset embryos were examined. CRISPR/nuclease was more effective than CRISPR/mRNA in avoiding mosai...
1 CitationsSource
#1Yoon Young Kim (SNU: Seoul National University)H-Index: 34
#2Byeong Cheol KangH-Index: 14
Last. 구승엽H-Index: 23
view all 8 authors...
The in vitro maturation of oocytes is frequently used as an assisted reproductive technique (ART), and has been successfully established in humans and rodents. To overcome the limitations of ART, novel procedures for the in vitro maturation of early follicles are emerging. During the follicle isolation procedure, the unintended rupture of each follicle leads to a release of extra oocytes. Such oocytes, which are obtained during follicle isolation from marmosets, can be used for early maturation ...
2 CitationsSource
#1Jonas AdrianH-Index: 2
Last. Christof R. HauckH-Index: 37
view all 5 authors...
Summary The selective pressure by infectious agents is a major driving force in the evolution of humans and other mammals. Members of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family serve as receptors for bacterial pathogens of the genera Haemophilus, Helicobacter, Neisseria, and Moraxella, which engage CEACAMs via distinct surface adhesins. While microbial attachment to epithelial CEACAMs facilitates host colonization, recognition by CEACAM3, a phagocytic receptor ex...
3 CitationsSource
#1Eri Tabata (Kogakuin University)H-Index: 5
#2Akinori Kashimura (Kogakuin University)H-Index: 8
Last. Fumitaka Oyama (Kogakuin University)H-Index: 34
view all 11 authors...
Chitin is a polymer of N-acetyl-D-glucosamine (GlcNAc) and a main constituent of insects’ exoskeleton. Insects are rich in protein with high energy conversion efficiency. Recently, we have reported that acidic chitinases (Chia) act as digestive enzymes in mouse, pig and chicken (omnivorous) but not in dog (carnivorous) and bovine (herbivorous), indicating that feeding behavior affects Chia expression levels, and determines chitin digestibility in the particular animals. Common marmoset (Callithr...
2 CitationsSource
#1N. Schmid (LMU: Ludwig Maximilian University of Munich)H-Index: 3
#2Jan Bernd StöcklH-Index: 2
Last. Artur Mayerhofer (LMU: Ludwig Maximilian University of Munich)H-Index: 37
view all 11 authors...
STUDY QUESTION: Are monkey testicular peritubular cells (MKTPCs) from the common marmoset monkey (Gallithrix jacchus) a suitable translational model for the study of human testicular peritubular cells (HTPCs)? A SUMMARY ANSWER: MKTPCs can be isolated and propagated in vitro, retain characteristic markers for testicular peritubular cells and their proteome strongly (correlation coefficient of 0.78) overlaps with the proteome of HTPCs. WHAT IS KNOWN ALREADY: Smooth-muscle-like peritubular cells fo...
5 CitationsSource
#1Bo Zhou (Stanford University)H-Index: 21
#2Steve S. Ho (Stanford University)H-Index: 3
Last. Alexander E. Urban (Stanford University)H-Index: 31
view all 13 authors...
Due to anatomical and physiological similarities to humans, the common marmoset (Callithrix jacchus), a non-human primate, is an ideal organism for the study of many human diseases. Researchers are currently leveraging genome-editing technologies such as CRISPR/Cas9 to genetically engineer marmosets for the in vivo biomedical modeling of human neuropsychiatric and neurodegenerative diseases. Several marmoset embryonic stem cell (ESC) lines and induced pluripotent stem cell (iPSC) lines establish...
#1Hideyuki Okano (Keio: Keio University)H-Index: 112
#2Noriyuki Kishi (Keio: Keio University)H-Index: 11
Although mice have been the most frequently used experimental animals in many research fields due to well-established gene manipulation techniques, recent evidence has revealed that rodent models do not always recapitulate pathophysiology of human neurological and psychiatric diseases due to the differences between humans and rodents. The recent developments in gene manipulation of non-human primate have been attracting much attention in the biomedical research field, because non-human primates ...
12 CitationsSource