Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement
Identifieur interne : 000B32 ( Main/Exploration ); précédent : 000B31; suivant : 000B33Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement
Auteurs : Sanzhen Liu [États-Unis] ; Jun Zheng [République populaire de Chine] ; Pierre Migeon [États-Unis] ; Jie Ren [États-Unis] ; Ying Hu [États-Unis] ; Cheng He [République populaire de Chine] ; Hongjun Liu ; Junjie Fu [République populaire de Chine] ; Frank F. White [États-Unis] ; Christopher Toomajian [États-Unis] ; Guoying Wang [République populaire de Chine]Source :
- Scientific Reports [ 2045-2322 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Ribosomal.
- genetics : Zea mays.
- methods : Genomics.
- Alleles, Chromosome Mapping, Domestication, Evolution, Molecular, Gene Dosage, Genome, Plant, Inbreeding, Quantitative Trait Loci, Repetitive Sequences, Nucleic Acid.
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
Url:
DOI: 10.1038/srep42444
PubMed: 28186206
PubMed Central: 5301235
Affiliations:
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Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement</title><author><name sortKey="Liu, Sanzhen" sort="Liu, Sanzhen" uniqKey="Liu S" first="Sanzhen" last="Liu">Sanzhen Liu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Plant Pathology, Kansas State University</institution>, Manhattan, KS, 66506,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zheng, Jun" sort="Zheng, Jun" uniqKey="Zheng J" first="Jun" last="Zheng">Jun Zheng</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Crop Science, Chinese Academy of Agricultural Sciences</institution>, Beijing 100081,<country>P.R.China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Migeon, Pierre" sort="Migeon, Pierre" uniqKey="Migeon P" first="Pierre" last="Migeon">Pierre Migeon</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Plant Pathology, Kansas State University</institution>, Manhattan, KS, 66506,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ren, Jie" sort="Ren, Jie" uniqKey="Ren J" first="Jie" last="Ren">Jie Ren</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Plant Pathology, Kansas State University</institution>, Manhattan, KS, 66506,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hu, Ying" sort="Hu, Ying" uniqKey="Hu Y" first="Ying" last="Hu">Ying Hu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Plant Pathology, Kansas State University</institution>, Manhattan, KS, 66506,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="He, Cheng" sort="He, Cheng" uniqKey="He C" first="Cheng" last="He">Cheng He</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Crop Science, Chinese Academy of Agricultural Sciences</institution>, Beijing 100081,<country>P.R.China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Hongjun" sort="Liu, Hongjun" uniqKey="Liu H" first="Hongjun" last="Liu">Hongjun Liu</name><affiliation><nlm:aff id="a3"><institution>State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology</institution>, Taian 271018,<country>P.R. China</country></nlm:aff><wicri:noCountry code="nlm country">P.R. China</wicri:noCountry></affiliation><affiliation><nlm:aff id="a4"><institution>College of Life Sciences, Shandong Agricultural University</institution>, Taian 271018,<country>P.R. China</country></nlm:aff><wicri:noCountry code="nlm country">P.R. China</wicri:noCountry></affiliation></author><author><name sortKey="Fu, Junjie" sort="Fu, Junjie" uniqKey="Fu J" first="Junjie" last="Fu">Junjie Fu</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Crop Science, Chinese Academy of Agricultural Sciences</institution>, Beijing 100081,<country>P.R.China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="White, Frank F" sort="White, Frank F" uniqKey="White F" first="Frank F." last="White">Frank F. White</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Department of Plant Pathology, University of Florida</institution>, Gainesville, FL, 32611,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Toomajian, Christopher" sort="Toomajian, Christopher" uniqKey="Toomajian C" first="Christopher" last="Toomajian">Christopher Toomajian</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Plant Pathology, Kansas State University</institution>, Manhattan, KS, 66506,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Guoying" sort="Wang, Guoying" uniqKey="Wang G" first="Guoying" last="Wang">Guoying Wang</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Crop Science, Chinese Academy of Agricultural Sciences</institution>, Beijing 100081,<country>P.R.China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Chromosome Mapping</term><term>Domestication</term><term>Evolution, Molecular</term><term>Gene Dosage</term><term>Genome, Plant</term><term>Genomics (methods)</term><term>Inbreeding</term><term>Quantitative Trait Loci</term><term>RNA, Ribosomal (genetics)</term><term>Repetitive Sequences, Nucleic Acid</term><term>Zea mays (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ribosomique (génétique)</term><term>Allèles</term><term>Cartographie chromosomique</term><term>Croisement consanguin</term><term>Domestication</term><term>Dosage génique</term><term>Génome végétal</term><term>Génomique ()</term><term>Locus de caractère quantitatif</term><term>Séquences répétées d'acides nucléiques</term><term>Zea mays (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Ribosomal</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN ribosomique</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Chromosome Mapping</term><term>Domestication</term><term>Evolution, Molecular</term><term>Gene Dosage</term><term>Genome, Plant</term><term>Inbreeding</term><term>Quantitative Trait Loci</term><term>Repetitive Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Cartographie chromosomique</term><term>Croisement consanguin</term><term>Domestication</term><term>Dosage génique</term><term>Génome végétal</term><term>Génomique</term><term>Locus de caractère quantitatif</term><term>Séquences répétées d'acides nucléiques</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gore, M A" uniqKey="Gore M">M. A. Gore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schnable, P S" uniqKey="Schnable P">P. S. Schnable</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lu, F" uniqKey="Lu F">F. Lu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barbazuk, W B" uniqKey="Barbazuk W">W. B. Barbazuk</name></author><author><name sortKey="Emrich, S J" uniqKey="Emrich S">S. J. 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White</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Zheng, Jun" sort="Zheng, Jun" uniqKey="Zheng J" first="Jun" last="Zheng">Jun Zheng</name></noRegion><name sortKey="Fu, Junjie" sort="Fu, Junjie" uniqKey="Fu J" first="Junjie" last="Fu">Junjie Fu</name><name sortKey="He, Cheng" sort="He, Cheng" uniqKey="He C" first="Cheng" last="He">Cheng He</name><name sortKey="Wang, Guoying" sort="Wang, Guoying" uniqKey="Wang G" first="Guoying" last="Wang">Guoying Wang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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