A willow sex chromosome reveals convergent evolution of complex palindromic repeats.
Identifieur interne : 000584 ( Main/Exploration ); précédent : 000583; suivant : 000585A willow sex chromosome reveals convergent evolution of complex palindromic repeats.
Auteurs : Ran Zhou [États-Unis] ; David Macaya-Sanz [États-Unis] ; Craig H. Carlson [États-Unis] ; Jeremy Schmutz [États-Unis] ; Jerry W. Jenkins [États-Unis] ; David Kudrna [États-Unis] ; Aditi Sharma [États-Unis] ; Laura Sandor [États-Unis] ; Shengqiang Shu [États-Unis] ; Kerrie Barry [États-Unis] ; Gerald A. Tuskan [États-Unis] ; Tao Ma [République populaire de Chine] ; Jianquan Liu [République populaire de Chine] ; Matthew Olson [États-Unis] ; Lawrence B. Smart [États-Unis] ; Stephen P. Difazio [États-Unis]Source :
- Genome biology [ 1474-760X ] ; 2020.
Abstract
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.
DOI: 10.1186/s13059-020-1952-4
PubMed: 32059685
PubMed Central: PMC7023750
Affiliations:
- République populaire de Chine, États-Unis
- Alabama, Arizona, Californie, État de New York
- Ithaca (New York)
- Université Cornell
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Jenkins</name><affiliation wicri:level="2"><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>HudsonAlpha Institute of Biotechnology, Huntsville, AL</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Kudrna, David" sort="Kudrna, David" uniqKey="Kudrna D" first="David" last="Kudrna">David Kudrna</name><affiliation wicri:level="2"><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ</wicri:regionArea><placeName><region type="state">Arizona</region></placeName></affiliation></author><author><name sortKey="Sharma, Aditi" sort="Sharma, Aditi" uniqKey="Sharma A" first="Aditi" last="Sharma">Aditi Sharma</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sandor, Laura" sort="Sandor, Laura" uniqKey="Sandor L" first="Laura" last="Sandor">Laura Sandor</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065</wicri:regionArea><wicri:noRegion>610065</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065</wicri:regionArea><wicri:noRegion>610065</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000</wicri:regionArea><wicri:noRegion>730000</wicri:noRegion></affiliation></author><author><name sortKey="Olson, Matthew" sort="Olson, Matthew" uniqKey="Olson M" first="Matthew" last="Olson">Matthew Olson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131</wicri:regionArea><wicri:noRegion>79409-3131</wicri:noRegion></affiliation></author><author><name sortKey="Smart, Lawrence B" sort="Smart, Lawrence B" uniqKey="Smart L" first="Lawrence B" last="Smart">Lawrence B. Smart</name><affiliation wicri:level="4"><nlm:affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456</wicri:regionArea><orgName type="university">Université Cornell</orgName><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA. spdifazio@mail.wvu.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057</wicri:regionArea><wicri:noRegion>26506-6057</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32059685</idno><idno type="pmid">32059685</idno><idno type="doi">10.1186/s13059-020-1952-4</idno><idno type="pmc">PMC7023750</idno><idno type="wicri:Area/Main/Corpus">000457</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000457</idno><idno type="wicri:Area/Main/Curation">000457</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000457</idno><idno type="wicri:Area/Main/Exploration">000457</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A willow sex chromosome reveals convergent evolution of complex palindromic repeats.</title><author><name sortKey="Zhou, Ran" sort="Zhou, Ran" uniqKey="Zhou R" first="Ran" last="Zhou">Ran Zhou</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057</wicri:regionArea><wicri:noRegion>26506-6057</wicri:noRegion></affiliation></author><author><name sortKey="Macaya Sanz, David" sort="Macaya Sanz, David" uniqKey="Macaya Sanz D" first="David" last="Macaya-Sanz">David Macaya-Sanz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057</wicri:regionArea><wicri:noRegion>26506-6057</wicri:noRegion></affiliation></author><author><name sortKey="Carlson, Craig H" sort="Carlson, Craig H" uniqKey="Carlson C" first="Craig H" last="Carlson">Craig H. Carlson</name><affiliation wicri:level="4"><nlm:affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456</wicri:regionArea><orgName type="university">Université Cornell</orgName><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation wicri:level="2"><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>HudsonAlpha Institute of Biotechnology, Huntsville, AL</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Jenkins, Jerry W" sort="Jenkins, Jerry W" uniqKey="Jenkins J" first="Jerry W" last="Jenkins">Jerry W. Jenkins</name><affiliation wicri:level="2"><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>HudsonAlpha Institute of Biotechnology, Huntsville, AL</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Kudrna, David" sort="Kudrna, David" uniqKey="Kudrna D" first="David" last="Kudrna">David Kudrna</name><affiliation wicri:level="2"><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ</wicri:regionArea><placeName><region type="state">Arizona</region></placeName></affiliation></author><author><name sortKey="Sharma, Aditi" sort="Sharma, Aditi" uniqKey="Sharma A" first="Aditi" last="Sharma">Aditi Sharma</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sandor, Laura" sort="Sandor, Laura" uniqKey="Sandor L" first="Laura" last="Sandor">Laura Sandor</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065</wicri:regionArea><wicri:noRegion>610065</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065</wicri:regionArea><wicri:noRegion>610065</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000</wicri:regionArea><wicri:noRegion>730000</wicri:noRegion></affiliation></author><author><name sortKey="Olson, Matthew" sort="Olson, Matthew" uniqKey="Olson M" first="Matthew" last="Olson">Matthew Olson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131</wicri:regionArea><wicri:noRegion>79409-3131</wicri:noRegion></affiliation></author><author><name sortKey="Smart, Lawrence B" sort="Smart, Lawrence B" uniqKey="Smart L" first="Lawrence B" last="Smart">Lawrence B. Smart</name><affiliation wicri:level="4"><nlm:affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456</wicri:regionArea><orgName type="university">Université Cornell</orgName><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA. spdifazio@mail.wvu.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057</wicri:regionArea><wicri:noRegion>26506-6057</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>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.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>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.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>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.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32059685</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>02</Month><Day>14</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol</ISOAbbreviation></Journal><ArticleTitle>A willow sex chromosome reveals convergent evolution of complex palindromic repeats.</ArticleTitle><Pagination><MedlinePgn>38</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13059-020-1952-4</ELocationID><Abstract><AbstractText Label="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.</AbstractText><AbstractText Label="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.</AbstractText><AbstractText Label="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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Ran</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macaya-Sanz</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carlson</LastName><ForeName>Craig H</ForeName><Initials>CH</Initials><AffiliationInfo><Affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmutz</LastName><ForeName>Jeremy</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jenkins</LastName><ForeName>Jerry W</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kudrna</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sharma</LastName><ForeName>Aditi</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sandor</LastName><ForeName>Laura</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shu</LastName><ForeName>Shengqiang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barry</LastName><ForeName>Kerrie</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Tao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jianquan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Olson</LastName><ForeName>Matthew</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smart</LastName><ForeName>Lawrence B</ForeName><Initials>LB</Initials><AffiliationInfo><Affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen P</ForeName><Initials>SP</Initials><Identifier Source="ORCID">0000-0003-4077-1590</Identifier><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA. spdifazio@mail.wvu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol</MedlineTA><NlmUniqueID>100960660</NlmUniqueID><ISSNLinking>1474-7596</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Gene conversion</Keyword><Keyword MajorTopicYN="Y">Genome</Keyword><Keyword MajorTopicYN="Y">Palindrome</Keyword><Keyword MajorTopicYN="Y">Salix</Keyword><Keyword MajorTopicYN="Y">Sex</Keyword><Keyword MajorTopicYN="Y">W chromosome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>07</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32059685</ArticleId><ArticleId IdType="doi">10.1186/s13059-020-1952-4</ArticleId><ArticleId 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York)</li></settlement><orgName><li>Université Cornell</li></orgName></list><tree><country name="États-Unis"><noRegion><name sortKey="Zhou, Ran" sort="Zhou, Ran" uniqKey="Zhou R" first="Ran" last="Zhou">Ran Zhou</name></noRegion><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><name sortKey="Carlson, Craig H" sort="Carlson, Craig H" uniqKey="Carlson C" first="Craig H" last="Carlson">Craig H. 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