IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-33366-x.html
   My bibliography  Save this article

High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation

Author

Listed:
  • Xiaoling Tong

    (Southwest University
    Southwest University)

  • Min-Jin Han

    (Southwest University
    Southwest University)

  • Kunpeng Lu

    (Southwest University)

  • Shuaishuai Tai

    (BGI Genomics, BGI-Shenzhen)

  • Shubo Liang

    (Southwest University)

  • Yucheng Liu

    (Chinese Academy of Sciences)

  • Hai Hu

    (Southwest University)

  • Jianghong Shen

    (Southwest University)

  • Anxing Long

    (Southwest University)

  • Chengyu Zhan

    (Southwest University)

  • Xin Ding

    (Southwest University)

  • Shuo Liu

    (Southwest University)

  • Qiang Gao

    (Southwest University)

  • Bili Zhang

    (Southwest University)

  • Linli Zhou

    (Southwest University
    Southwest University)

  • Duan Tan

    (Southwest University
    Southwest University)

  • Yajie Yuan

    (Southwest University)

  • Nangkuo Guo

    (Southwest University)

  • Yan-Hong Li

    (BGI Genomics, BGI-Shenzhen)

  • Zhangyan Wu

    (BGI Genomics, BGI-Shenzhen)

  • Lulu Liu

    (Southwest University)

  • Chunlin Li

    (Southwest University)

  • Yaru Lu

    (Southwest University)

  • Tingting Gai

    (Southwest University)

  • Yahui Zhang

    (Southwest University)

  • Renkui Yang

    (Chongqing Sericulture Science and Technology Research Institute)

  • Heying Qian

    (Jiangsu University of Science and Technology)

  • Yanqun Liu

    (Shenyang Agricultural University)

  • Jiangwen Luo

    (Southwest University)

  • Lu Zheng

    (Southwest University)

  • Jinghou Lou

    (Southwest University)

  • Yunwu Peng

    (Ankang University)

  • Weidong Zuo

    (Southwest University
    Southwest University)

  • Jiangbo Song

    (Southwest University)

  • Songzhen He

    (Southwest University)

  • Songyuan Wu

    (Southwest University
    Southwest University)

  • Yunlong Zou

    (Southwest University
    Southwest University)

  • Lei Zhou

    (Southwest University)

  • Lan Cheng

    (Southwest University
    Southwest University)

  • Yuxia Tang

    (Southwest University)

  • Guotao Cheng

    (Southwest University
    Southwest University)

  • Lianwei Yuan

    (Southwest University)

  • Weiming He

    (BGI Genomics, BGI-Shenzhen)

  • Jiabao Xu

    (BGI Genomics, BGI-Shenzhen)

  • Tao Fu

    (BGI Genomics, BGI-Shenzhen)

  • Yang Xiao

    (Guangdong Academy of Agricultural Sciences)

  • Ting Lei

    (Chongqing Sericulture Science and Technology Research Institute)

  • Anying Xu

    (Jiangsu University of Science and Technology)

  • Ye Yin

    (BGI Genomics, BGI-Shenzhen)

  • Jian Wang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Sciences)

  • Antónia Monteiro

    (National University of Singapore
    Science Division, Yale-NUS College)

  • Eric Westhof

    (Southwest University
    Université de Strasbourg)

  • Cheng Lu

    (Southwest University)

  • Zhixi Tian

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Wen Wang

    (Northwestern Polytechnical University
    Chinese Academy of Sciences)

  • Zhonghuai Xiang

    (Southwest University)

  • Fangyin Dai

    (Southwest University
    Southwest University)

Abstract

The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.

Suggested Citation

  • Xiaoling Tong & Min-Jin Han & Kunpeng Lu & Shuaishuai Tai & Shubo Liang & Yucheng Liu & Hai Hu & Jianghong Shen & Anxing Long & Chengyu Zhan & Xin Ding & Shuo Liu & Qiang Gao & Bili Zhang & Linli Zhou, 2022. "High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33366-x
    DOI: 10.1038/s41467-022-33366-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-33366-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-33366-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Junichi Yamaguchi & Yutaka Banno & Kazuei Mita & Kimiko Yamamoto & Toshiya Ando & Haruhiko Fujiwara, 2013. "Periodic Wnt1 expression in response to ecdysteroid generates twin-spot markings on caterpillars," Nature Communications, Nature, vol. 4(1), pages 1-9, June.
    2. Mahul Chakraborty & J. J. Emerson & Stuart J. Macdonald & Anthony D. Long, 2019. "Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    3. Zhikun Wu & Zehang Jiang & Tong Li & Chuanbo Xie & Liansheng Zhao & Jiaqi Yang & Shuai Ouyang & Yizhi Liu & Tao Li & Zhi Xie, 2021. "Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Agnieszka A. Golicz & Philipp E. Bayer & Guy C. Barker & Patrick P. Edger & HyeRan Kim & Paula A. Martinez & Chon Kit Kenneth Chan & Anita Severn-Ellis & W. Richard McCombie & Isobel A. P. Parkin & An, 2016. "The pangenome of an agronomically important crop plant Brassica oleracea," Nature Communications, Nature, vol. 7(1), pages 1-8, December.
    5. Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    6. Peter H. Sudmant & Tobias Rausch & Eugene J. Gardner & Robert E. Handsaker & Alexej Abyzov & John Huddleston & Yan Zhang & Kai Ye & Goo Jun & Markus Hsi-Yang Fritz & Miriam K. Konkel & Ankit Malhotra , 2015. "An integrated map of structural variation in 2,504 human genomes," Nature, Nature, vol. 526(7571), pages 75-81, October.
    7. Ryan L. Collins & Harrison Brand & Konrad J. Karczewski & Xuefang Zhao & Jessica Alföldi & Laurent C. Francioli & Amit V. Khera & Chelsea Lowther & Laura D. Gauthier & Harold Wang & Nicholas A. Watts , 2020. "A structural variation reference for medical and population genetics," Nature, Nature, vol. 581(7809), pages 444-451, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ramesh Rajaby & Dong-Xu Liu & Chun Hang Au & Yuen-Ting Cheung & Amy Yuet Ting Lau & Qing-Yong Yang & Wing-Kin Sung, 2023. "INSurVeyor: improving insertion calling from short read sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Can Luo & Yichen Henry Liu & Xin Maizie Zhou, 2024. "VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    3. Jinlong Shi & Zhilong Jia & Jinxiu Sun & Xiaoreng Wang & Xiaojing Zhao & Chenghui Zhao & Fan Liang & Xinyu Song & Jiawei Guan & Xue Jia & Jing Yang & Qi Chen & Kang Yu & Qian Jia & Jing Wu & Depeng Wa, 2023. "Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    4. Yichen Henry Liu & Can Luo & Staunton G. Golding & Jacob B. Ioffe & Xin Maizie Zhou, 2024. "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    5. Cristian Groza & Carl Schwendinger-Schreck & Warren A. Cheung & Emily G. Farrow & Isabelle Thiffault & Juniper Lake & William B. Rizzo & Gilad Evrony & Tom Curran & Guillaume Bourque & Tomi Pastinen, 2024. "Pangenome graphs improve the analysis of structural variants in rare genetic diseases," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Yirong Shi & Yiwei Niu & Peng Zhang & Huaxia Luo & Shuai Liu & Sijia Zhang & Jiajia Wang & Yanyan Li & Xinyue Liu & Tingrui Song & Tao Xu & Shunmin He, 2023. "Characterization of genome-wide STR variation in 6487 human genomes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Marsha M. Wheeler & Adrienne M. Stilp & Shuquan Rao & Bjarni V. Halldórsson & Doruk Beyter & Jia Wen & Anna V. Mihkaylova & Caitlin P. McHugh & John Lane & Min-Zhi Jiang & Laura M. Raffield & Goo Jun , 2022. "Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    8. Ludovica Montanucci & David Lewis-Smith & Ryan L. Collins & Lisa-Marie Niestroj & Shridhar Parthasarathy & Julie Xian & Shiva Ganesan & Marie Macnee & Tobias Brünger & Rhys H. Thomas & Michael Talkows, 2023. "Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    9. Zhikun Wu & Zehang Jiang & Tong Li & Chuanbo Xie & Liansheng Zhao & Jiaqi Yang & Shuai Ouyang & Yizhi Liu & Tao Li & Zhi Xie, 2021. "Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    10. Liyuan Zhou & Qiongzi Qiu & Qing Zhou & Jianwei Li & Mengqian Yu & Kezhen Li & Lingling Xu & Xiaohui Ke & Haiming Xu & Bingjian Lu & Hui Wang & Weiguo Lu & Pengyuan Liu & Yan Lu, 2022. "Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    11. Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    12. Jinhyun Kim & Sungsik Kim & Huiran Yeom & Seo Woo Song & Kyoungseob Shin & Sangwook Bae & Han Suk Ryu & Ji Young Kim & Ahyoun Choi & Sumin Lee & Taehoon Ryu & Yeongjae Choi & Hamin Kim & Okju Kim & Yu, 2023. "Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    13. Yingyan Yu & Zhen Zhang & Xiaorui Dong & Ruixin Yang & Zhongqu Duan & Zhen Xiang & Jun Li & Guichao Li & Fazhe Yan & Hongzhang Xue & Du Jiao & Jinyuan Lu & Huimin Lu & Wenmin Zhang & Yangzhen Wei & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    14. Huiying He & Yue Leng & Xinglan Cao & Yiwang Zhu & Xiaoxia Li & Qiaoling Yuan & Bin Zhang & Wenchuang He & Hua Wei & Xiangpei Liu & Qiang Xu & Mingliang Guo & Hong Zhang & Longbo Yang & Yang Lv & Xian, 2024. "The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    15. Xue Gao & Sheng Wang & Yan-Fen Wang & Shuang Li & Shi-Xin Wu & Rong-Ge Yan & Yi-Wen Zhang & Rui-Dong Wan & Zhen He & Ren-De Song & Xin-Quan Zhao & Dong-Dong Wu & Qi-En Yang, 2022. "Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    16. Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    17. Zhuoran Xu & Quan Li & Luigi Marchionni & Kai Wang, 2023. "PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    18. Qiliang Ding & Matthew M. Edwards & Ning Wang & Xiang Zhu & Alexa N. Bracci & Michelle L. Hulke & Ya Hu & Yao Tong & Joyce Hsiao & Christine J. Charvet & Sulagna Ghosh & Robert E. Handsaker & Kevin Eg, 2021. "The genetic architecture of DNA replication timing in human pluripotent stem cells," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    19. Neik, T. X. & Siddique, K. H. M. & Mayes, S. & Edwards, D. & Batley, J. & Mabhaudhi, Tafadzwanashe & Song, B. K. & Massawe, F., 2023. "Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis," Papers published in Journals (Open Access), International Water Management Institute, pages 1-7:1124640.
    20. Naser Ansari-Pour & Yonglan Zheng & Toshio F. Yoshimatsu & Ayodele Sanni & Mustapha Ajani & Jean-Baptiste Reynier & Avraam Tapinos & Jason J. Pitt & Stefan Dentro & Anna Woodard & Padma Sheila Rajagop, 2021. "Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes," Nature Communications, Nature, vol. 12(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33366-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.