Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

View ORCID ProfileCheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, View ORCID ProfileGregg W.C. Thomas, Mengya Zhao, Xingtan Zhang, View ORCID ProfileIrwin Jungreis, Manolis Kellis, Saverio Vicario, View ORCID ProfileIgor V. Sharakhov, Semen M. Bondarenko, View ORCID ProfileMartin Hasselmann, Chang N Kim, Benedict Paten, View ORCID ProfileLuca Penso-Dolfin, Li Wang, View ORCID ProfileYuxiao Chang, Qiang Gao, Ling Ma, View ORCID ProfileLina Ma, Zhang Zhang, Hongbo Zhang, Huahao Zhang, View ORCID ProfileLivio Ruzzante, Hugh M. Robertson, View ORCID ProfileYihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Ben M. Sadd, Gang Cao, Ze Zhang, View ORCID ProfileMatthew Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, View ORCID ProfileRobert M. Waterhouse, Rachel Lockridge Mueller
doi: https://doi.org/10.1101/2020.05.29.122879
Cheng Sun
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Cheng Sun
  • For correspondence: suncheng@caas.cn robert.waterhouse@unil.ch
Jiaxing Huang
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yun Wang
2School of Life Sciences, Chongqing University, Chongqing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiaomeng Zhao
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Long Su
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gregg W.C. Thomas
3Division of Biological Sciences, University of Montana, Missoula, Montana, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gregg W.C. Thomas
Mengya Zhao
4State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xingtan Zhang
5Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Irwin Jungreis
6MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA
7Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Irwin Jungreis
Manolis Kellis
6MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA
7Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Saverio Vicario
8Institute of Atmospheric Pollution Research-Italian National Research Council C/O Department of Physics, University of Bari, via Orabona 4, 70125 Bari, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Igor V. Sharakhov
9Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, 24061, USA
10Department of Cytology and Genetics, Tomsk State University, Tomsk 634050, Russian Federation
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Igor V. Sharakhov
Semen M. Bondarenko
9Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, 24061, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin Hasselmann
11Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martin Hasselmann
Chang N Kim
12UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benedict Paten
12UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luca Penso-Dolfin
13German Cancer Research Center, Heidelberg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Luca Penso-Dolfin
Li Wang
14Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yuxiao Chang
14Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yuxiao Chang
Qiang Gao
15BGI Genomics, BGI-Shenzhen, Shenzhen, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ling Ma
15BGI Genomics, BGI-Shenzhen, Shenzhen, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lina Ma
16China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lina Ma
Zhang Zhang
16China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hongbo Zhang
2School of Life Sciences, Chongqing University, Chongqing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Huahao Zhang
17College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Livio Ruzzante
18Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Livio Ruzzante
Hugh M. Robertson
19Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yihui Zhu
20Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yihui Zhu
Yanjie Liu
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Huipeng Yang
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lele Ding
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Quangui Wang
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Weilin Xu
1Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cheng Liang
21Institute of Sericultural and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael W. Itgen
22Department of Biology, Colorado State University, Fort collins, CO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lauren Mee
23Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ben M. Sadd
24School of Biological Sciences, Illinois State University, Normal, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gang Cao
4State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ze Zhang
2School of Life Sciences, Chongqing University, Chongqing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew Hahn
25Department of Biology & Department of Computer Science, Indiana University, Bloomington, IN, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Matthew Hahn
Sarah Schaack
26Department of Biology, Reed College, Portland, Oregon, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Seth M. Barribeau
23Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul H. Williams
27Department of Life Sciences, Natural History Museum, London, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert M. Waterhouse
18Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Robert M. Waterhouse
  • For correspondence: suncheng@caas.cn robert.waterhouse@unil.ch
Rachel Lockridge Mueller
22Department of Biology, Colorado State University, Fort collins, CO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary lifecycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. These high-quality genomic resources capture natural genetic and phenotypic variation across bumblebees, offering new opportunities to advance our understanding of their remarkable ecological success and to identify and manage current and future threats.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted May 31, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators
Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W.C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, Manolis Kellis, Saverio Vicario, Igor V. Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Zhang Zhang, Hongbo Zhang, Huahao Zhang, Livio Ruzzante, Hugh M. Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Ben M. Sadd, Gang Cao, Ze Zhang, Matthew Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, Robert M. Waterhouse, Rachel Lockridge Mueller
bioRxiv 2020.05.29.122879; doi: https://doi.org/10.1101/2020.05.29.122879
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators
Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W.C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, Manolis Kellis, Saverio Vicario, Igor V. Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Zhang Zhang, Hongbo Zhang, Huahao Zhang, Livio Ruzzante, Hugh M. Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Ben M. Sadd, Gang Cao, Ze Zhang, Matthew Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, Robert M. Waterhouse, Rachel Lockridge Mueller
bioRxiv 2020.05.29.122879; doi: https://doi.org/10.1101/2020.05.29.122879

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3602)
  • Biochemistry (7567)
  • Bioengineering (5522)
  • Bioinformatics (20782)
  • Biophysics (10325)
  • Cancer Biology (7978)
  • Cell Biology (11635)
  • Clinical Trials (138)
  • Developmental Biology (6602)
  • Ecology (10200)
  • Epidemiology (2065)
  • Evolutionary Biology (13611)
  • Genetics (9539)
  • Genomics (12844)
  • Immunology (7919)
  • Microbiology (19538)
  • Molecular Biology (7657)
  • Neuroscience (42081)
  • Paleontology (308)
  • Pathology (1257)
  • Pharmacology and Toxicology (2201)
  • Physiology (3267)
  • Plant Biology (7038)
  • Scientific Communication and Education (1294)
  • Synthetic Biology (1951)
  • Systems Biology (5426)
  • Zoology (1116)