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      Draft Genome of the European Mouflon ( Ovis orientalis musimon)

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          Abstract

          Mouflon ( Ovis orientalis) with its huge and beautiful horns is considered as one of the ancestors of domesticated sheep. The European mouflon ( Ovis orientalis musimon) is in the Asiatic mouflon ( O. orientalis) clade. In order to provide novel genome information for mouflon, moreover promote genetic analysis of genus Ovis both domestic and wild, we propose to sequence the mouflon genome. We assembled the highly heterozygous mouflon genome based on Illumina HiSeq platform using the next-generation sequencing technology. Finally, the draft genome we accessed approximately 2.69 Gb (42.15% GC), while N50 sizes of contig and scaffold are 110.1 kb and 10.4 Mb, respectively. The contiguity of this assembly is obviously better than earlier versions. Further analyses predicted 20,814 protein-coding genes in the mouflon genome and 12,390 shared gene families among bovine species. It is estimated that the divergence time between O. orientalis musimon and Ovis aries was 7.6 million years ago. The draft mouflon genome assembly will provide data support and theoretical basis for various investigations of the genus Ovis species in future.

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          Most cited references51

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

            Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
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              Tandem repeats finder: a program to analyze DNA sequences.

              G. Benson (1999)
              A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                19 November 2020
                2020
                : 11
                : 533611
                Affiliations
                [1] 1College of Animal Science, Inner Mongolia Agricultural University , Hohhot, China
                [2] 2Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region , Hohhot, China
                [3] 3Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture , Hohhot, China
                [4] 4Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region , Hohhot, China
                [5] 5State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China
                [6] 6NOWBIO Technology Co. Ltd , Kunming, China
                [7] 7College of Biological Big Data, Yunnan Agricultural University , Kunming, China
                [8] 8Yunnan Research Institute for Local Plateau Agriculture and Industry , Kunming, China
                [9] 9Daqingshan Wild Animal Park, Hohhot Gardens Management Bureau , Hohhot, China
                [10] 10Key Laboratory for Space Bioscience and Biotechnology, Center for Ecological and Environmental Sciences, Northwestern Polytechnical University , Xi’an, China
                Author notes

                Edited by: Göran Andersson, Swedish University of Agricultural Sciences, Sweden

                Reviewed by: Xiaozhu Wang, Auburn University, United States; Jennifer R.S. Meadows, Uppsala University, Sweden

                *Correspondence: Yang Dong, loyalyang@ 123456163.com

                These authors have contributed equally to this work

                This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2020.533611
                7710762
                ad53a694-86b7-4ba6-b097-46eb61cb021f
                Copyright © 2020 Su, Qiao, Gao, Li, Jiang, Chen, Fan, Zheng, Zhang, Liu, Wang, Wang, Wang, Wan, Dong and Li.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 February 2020
                : 26 October 2020
                Page count
                Figures: 0, Tables: 2, Equations: 0, References: 51, Pages: 7, Words: 0
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31860637
                Award ID: 31660639
                Funded by: Research Program of Science and Technology at Universities of Inner Mongolia Autonomous Region 10.13039/501100013147
                Award ID: 2019-1356
                Funded by: Agriculture Research System of China 10.13039/501100010203
                Award ID: CARS-39-06
                Categories
                Genetics
                Original Research

                Genetics
                mouflon,ovis orientalis musimon,illumina sequencing,de novo genome assembly,genus ovis
                Genetics
                mouflon, ovis orientalis musimon, illumina sequencing, de novo genome assembly, genus ovis

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