Organellar genome assembly methods and comparative analysis of horticultural plants.
Identifieur interne : 000781 ( Main/Corpus ); précédent : 000780; suivant : 000782Organellar genome assembly methods and comparative analysis of horticultural plants.
Auteurs : Xuelin Wang ; Feng Cheng ; Dekai Rohlsen ; Changwei Bi ; Chunyan Wang ; Yiqing Xu ; Suyun Wei ; Qiaolin Ye ; Tongming Yin ; Ning YeSource :
- Horticulture research [ 2052-7276 ] ; 2018.
Abstract
Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows-Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.
DOI: 10.1038/s41438-017-0002-1
PubMed: 29423233
PubMed Central: PMC5798811
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FL 33612 USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><affiliation><nlm:affiliation>3School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chunyan" sort="Wang, Chunyan" uniqKey="Wang C" first="Chunyan" last="Wang">Chunyan Wang</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wei, Suyun" sort="Wei, Suyun" uniqKey="Wei S" first="Suyun" last="Wei">Suyun Wei</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Qiaolin" sort="Ye, Qiaolin" uniqKey="Ye Q" first="Qiaolin" last="Ye">Qiaolin Ye</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name><affiliation><nlm:affiliation>4College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29423233</idno><idno type="pmid">29423233</idno><idno type="doi">10.1038/s41438-017-0002-1</idno><idno type="pmc">PMC5798811</idno><idno type="wicri:Area/Main/Corpus">000781</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000781</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Organellar genome assembly methods and comparative analysis of horticultural plants.</title><author><name sortKey="Wang, Xuelin" sort="Wang, Xuelin" uniqKey="Wang X" first="Xuelin" last="Wang">Xuelin Wang</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Cheng, Feng" sort="Cheng, Feng" uniqKey="Cheng F" first="Feng" last="Cheng">Feng Cheng</name><affiliation><nlm:affiliation>2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL 33612 USA.</nlm:affiliation></affiliation></author><author><name sortKey="Rohlsen, Dekai" sort="Rohlsen, Dekai" uniqKey="Rohlsen D" first="Dekai" last="Rohlsen">Dekai Rohlsen</name><affiliation><nlm:affiliation>2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL 33612 USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><affiliation><nlm:affiliation>3School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chunyan" sort="Wang, Chunyan" uniqKey="Wang C" first="Chunyan" last="Wang">Chunyan Wang</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wei, Suyun" sort="Wei, Suyun" uniqKey="Wei S" first="Suyun" last="Wei">Suyun Wei</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Qiaolin" sort="Ye, Qiaolin" uniqKey="Ye Q" first="Qiaolin" last="Ye">Qiaolin Ye</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name><affiliation><nlm:affiliation>4College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name><affiliation><nlm:affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Horticulture research</title><idno type="ISSN">2052-7276</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows-Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, <i>Salix suchowensis</i>, and a fruit tree, <i>Ziziphus jujuba</i>, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">29423233</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2052-7276</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>Horticulture research</Title><ISOAbbreviation>Hortic Res</ISOAbbreviation></Journal><ArticleTitle>Organellar genome assembly methods and comparative analysis of horticultural plants.</ArticleTitle><Pagination><MedlinePgn>3</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41438-017-0002-1</ELocationID><Abstract><AbstractText>Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows-Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, <i>Salix suchowensis</i>, and a fruit tree, <i>Ziziphus jujuba</i>, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xuelin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Feng</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL 33612 USA.</Affiliation><Identifier Source="ISNI">0000 0001 2353 285X</Identifier><Identifier Source="GRID">grid.170693.a</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rohlsen</LastName><ForeName>Dekai</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL 33612 USA.</Affiliation><Identifier Source="ISNI">0000 0001 2353 285X</Identifier><Identifier Source="GRID">grid.170693.a</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bi</LastName><ForeName>Changwei</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>3School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="ISNI">0000 0004 1761 0489</Identifier><Identifier Source="GRID">grid.263826.b</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Chunyan</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yiqing</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Suyun</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Qiaolin</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Tongming</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>4College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Ning</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.</Affiliation><Identifier Source="GRID">grid.410625.4</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>01</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Hortic Res</MedlineTA><NlmUniqueID>101655540</NlmUniqueID><ISSNLinking>2052-7276</ISSNLinking></MedlineJournalInfo><CoiStatement>The authors declare that they have no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>05</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>11</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>11</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>2</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>2</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>2</Month><Day>10</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId 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