A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Zhou, Ran; Macaya-Sanz, David; Carlson, Craig H.; Schmutz, Jeremy; Jenkins, Jerry W.; Kudrna, David; Sharma, Aditi; Sandor, Laura; Shu, Shengqiang; Barry, Kerrie; Tuskan, Gerald A.; Ma, Tao; Liu, Jianquan; Olson, Matthew; Smart, Lawrence B.; DiFazio, Stephen P.

doi:10.1186/s13059-020-1952-4

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Journal Article · Fri Feb 14 04:00:00 EST 2020 · Genome Biology (Online)

DOI:https://doi.org/10.1186/s13059-020-1952-4· OSTI ID:1626951

Zhou, Ran ^[1]; Macaya-Sanz, David ^[2]; Carlson, Craig H. ^[3]; Schmutz, Jeremy ^[4]; Jenkins, Jerry W. ^[5]; Kudrna, David ^[6]; Sharma, Aditi ^[7]; Sandor, Laura ^[7]; Shu, Shengqiang ^[7]; Barry, Kerrie ^[7]; Tuskan, Gerald A. ^[8]; Ma, Tao ^[9]; Liu, Jianquan ^[10]; Olson, Matthew ^[11]; Smart, Lawrence B. ^[3]; ^[2]

West Virginia Univ., Morgantown, WV (United States); DOE/OSTI
West Virginia Univ., Morgantown, WV (United States)
Cornell Univ., Geneva, NY (United States). New York State Agricultural Experiment Station
HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
Univ. of Arizona, Tucson, AZ (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sichuan Univ., Chengdu (China)
Sichuan Univ., Chengdu (China); Lanzhou Univ. (China)
Texas Tech Univ., Lubbock, TX (United States)

Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); National Natural Science Foundation of China (NSFC); National Key Research and Development Program of China; National Key Project for Basic Research

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626951

Alternate ID(s):: OSTI ID: 1648998

Journal Information:: Genome Biology (Online), Journal Name: Genome Biology (Online) Journal Issue: 1 Vol. 21; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Salix
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sex

Additional file 1 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859030 The current record is supplemented by this dataset	dataset	January 2020
Additional file 1 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859030.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 2 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859033 The current record is supplemented by this text	text	January 2020
Additional file 2 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859033.v1 The current record is supplemented by this text	text	January 2020
Additional file 3 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859042 The current record is supplemented by this text	text	January 2020
Additional file 3 of A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.11859042.v1 The current record is supplemented by this text	text	January 2020
A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.c.4858245 The current record is supplemented by this collection	collection	January 2020
A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, Ran; Macaya-Sanz, David; Carlson, Craig https://doi.org/10.6084/m9.figshare.c.4858245.v1 The current record is supplemented by this collection	collection	January 2020

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

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