The sequence and de novo assembly of hog deer genome

Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome s...

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Published inScientific data Vol. 6; no. 1; p. 180305
Main Authors Wang, Wei, Yan, Hui-Juan, Chen, Shi-Yi, Li, Zhen-Zhen, Yi, Jun, Niu, Li-Li, Deng, Jia-Po, Chen, Wei-Gang, Pu, Yang, Jia, Xianbo, Qu, Yu, Chen, Ang, Zhong, Yan, Yu, Xin-Ming, Pang, Shuai, Huang, Wan-Long, Han, Yue, Liu, Guang-Jian, Yu, Jian-Qiu
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 08.01.2019
Nature Publishing Group
Subjects
631/208/726
631/601
Animals
Axis porcinus
Cervidae
China
Comparative analysis
Data Descriptor
Deer - genetics
DNA sequencing
Evolution
Genetic diversity
Genome
Genomes
Genomics
Humanities and Social Sciences
Kidneys
Molecular Sequence Annotation
multidisciplinary
Nucleotide sequence
Science
Sequence Analysis, DNA
Spleen
Whole genome sequencing
China
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Abstract Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae. Design Type(s) sequence assembly objective • sequence analysis objective • sequence annotation objective Measurement Type(s) whole genome sequencing Technology Type(s) DNA sequencing Factor Type(s) animal body part Sample Characteristic(s) Axis porcinus • blood • brain • heart • lung • liver • spleen • kidney Machine-accessible metadata file describing the reported data (ISA-Tab format)
AbstractList Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.
Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.Design Type(s)sequence assembly objective • sequence analysis objective • sequence annotation objectiveMeasurement Type(s)whole genome sequencingTechnology Type(s)DNA sequencingFactor Type(s)animal body partSample Characteristic(s)Axis porcinus • blood • brain • heart • lung • liver • spleen • kidneyMachine-accessible metadata file describing the reported data (ISA-Tab format)
Abstract Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.
Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae. Design Type(s) sequence assembly objective • sequence analysis objective • sequence annotation objective Measurement Type(s) whole genome sequencing Technology Type(s) DNA sequencing Factor Type(s) animal body part Sample Characteristic(s) Axis porcinus • blood • brain • heart • lung • liver • spleen • kidney Machine-accessible metadata file describing the reported data (ISA-Tab format)
Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.
Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.
ArticleNumber 180305
Author Han, Yue
Pu, Yang
Wang, Wei
Yan, Hui-Juan
Chen, Shi-Yi
Jia, Xianbo
Yu, Jian-Qiu
Qu, Yu
Yu, Xin-Ming
Li, Zhen-Zhen
Yi, Jun
Deng, Jia-Po
Chen, Ang
Huang, Wan-Long
Chen, Wei-Gang
Zhong, Yan
Pang, Shuai
Niu, Li-Li
Liu, Guang-Jian
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These authors contributed equally to this work.
W.W., G.J.L. and J.Q.Y. designed and supervised the study. J.Y., L.L.N., J.P.D., W.G.C., Y.P., X.J., Y.Q., A.C., Y.Z. and X.M.Y. prepared the samples. H.J.Y., S.Y.C., Z.Z.L., S.P., W.L.H. and Y.H. analyzed all sequencing data. W.W., H.J.Y., S.Y.C. and Z.Z.L. wrote the manuscript with the other authors’ helps. All authors revised the draft and approved the final manuscript.
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SSID ssj0001340570
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Snippet Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo...
Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo...
Abstract Hog deer ( Axis porcinus ) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades....
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StartPage 180305
SubjectTerms 631/208/726
631/601
Animals
Axis porcinus
Cervidae
China
Comparative analysis
Data Descriptor
Deer - genetics
DNA sequencing
Evolution
Genetic diversity
Genome
Genomes
Genomics
Humanities and Social Sciences
Kidneys
Molecular Sequence Annotation
multidisciplinary
Nucleotide sequence
Science
Sequence Analysis, DNA
Spleen
Whole genome sequencing
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Title The sequence and de novo assembly of hog deer genome
URI https://link.springer.com/article/10.1038/sdata.2018.305
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