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Improved maize reference genome with single-molecule technologies

Author

Listed:
  • Yinping Jiao

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Paul Peluso

    (Pacific Biosciences)

  • Jinghua Shi

    (BioNano Genomics)

  • Tiffany Liang

    (BioNano Genomics)

  • Michelle C. Stitzer

    (University of California, Davis)

  • Bo Wang

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Michael S. Campbell

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Joshua C. Stein

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Xuehong Wei

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Chen-Shan Chin

    (Pacific Biosciences)

  • Katherine Guill

    (USDA-ARS, Plant Genetics Research Unit)

  • Michael Regulski

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Sunita Kumari

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Andrew Olson

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Jonathan Gent

    (University of Georgia)

  • Kevin L. Schneider

    (University of Hawaii)

  • Thomas K. Wolfgruber

    (University of Hawaii)

  • Michael R. May

    (University of California)

  • Nathan M. Springer

    (University of Minnesota)

  • Eric Antoniou

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • W. Richard McCombie

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Gernot G. Presting

    (University of Hawaii)

  • Michael McMullen

    (USDA-ARS, Plant Genetics Research Unit)

  • Jeffrey Ross-Ibarra

    (Center for Population Biology, and Genome Center, University of California)

  • R. Kelly Dawe

    (University of Georgia)

  • Alex Hastie

    (BioNano Genomics)

  • David R. Rank

    (Pacific Biosciences)

  • Doreen Ware

    (Cold Spring Harbor Laboratory, Cold Spring Harbor
    USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University)

Abstract

An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize.

Suggested Citation

  • Yinping Jiao & Paul Peluso & Jinghua Shi & Tiffany Liang & Michelle C. Stitzer & Bo Wang & Michael S. Campbell & Joshua C. Stein & Xuehong Wei & Chen-Shan Chin & Katherine Guill & Michael Regulski & S, 2017. "Improved maize reference genome with single-molecule technologies," Nature, Nature, vol. 546(7659), pages 524-527, June.
    • Handle: RePEc:nat:nature:v:546:y:2017:i:7659:d:10.1038_nature22971
    DOI: 10.1038/nature22971
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    Citations

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    Cited by:

    1. Yibing Zeng & Julian Somers & Harrison S. Bell & Zuzana Vejlupkova & R. Kelly Dawe & John E. Fowler & Brad Nelms & Jonathan I. Gent, 2024. "Potent pollen gene regulation by DNA glycosylases in maize," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Yixue Bao & Qing Zhang & Jiangfeng Huang & Shengcheng Zhang & Wei Yao & Zehuai Yu & Zuhu Deng & Jiaxin Yu & Weilong Kong & Xikai Yu & Shan Lu & Yibin Wang & Ru Li & Yuhan Song & Chengwu Zou & Yuzhi Xu, 2024. "A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Feng Tong & Teng Wang & Na L. Gao & Ziying Liu & Kuiqing Cui & Yiqian Duan & Sicheng Wu & Yuhong Luo & Zhipeng Li & Chengjian Yang & Yixue Xu & Bo Lin & Liguo Yang & Alfredo Pauciullo & Deshun Shi & G, 2022. "The microbiome of the buffalo digestive tract," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Zhibin Chen & Zhaogui Zhang & Huairen Zhang & Kai Li & Darun Cai & Li Zhao & Juan Liu & Huabang Chen, 2022. "A pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Yuxin Fu & Wenxin Xiao & Lang Tian & Liangxing Guo & Guangjin Ma & Chen Ji & Yongcai Huang & Haihai Wang & Xingguo Wu & Tao Yang & Jiechen Wang & Jirui Wang & Yongrui Wu & Wenqin Wang, 2023. "Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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