Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut
Transcriptome resources can facilitate to increase yield and quality of walnuts. Finding the best transcriptome assembly has not been the subject of walnuts research as yet. This research generated 240,179,782 reads from 11 walnut leaves according to cDNA libraries. The reads provided a complete de...
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| Veröffentlicht in: | PloS one 2020-04, Vol.15 (4), p.e0232005-e0232005 |
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| creator | Sadat-Hosseini, Mohammad Bakhtiarizadeh, Mohammad Reza Boroomand, Naser Tohidfar, Masoud Vahdati, Kourosh |
| description | Transcriptome resources can facilitate to increase yield and quality of walnuts. Finding the best transcriptome assembly has not been the subject of walnuts research as yet. This research generated 240,179,782 reads from 11 walnut leaves according to cDNA libraries. The reads provided a complete de novo transcriptome assembly. Fifteen different transcriptome assemblies were constructed from five different well-known assemblers used in scientific literature with different k-mer lengths (Bridger, BinPacker, SOAPdenovo-Trans, Trinity and SPAdes) as well as two merging approaches (EvidentialGene and Transfuse). Based on the four quality metrics of assembly, the results indicated an efficiency in the process of merging the assemblies after being generated by de novo assemblers. Finally, EvidentialGene was recognized as the best assembler for the de novo assembly of the leaf transcriptome in walnut. Among a total number of 183,191 transcripts which were generated by EvidentialGene, there were 109,413 transcripts capable of protein potential (59.72%) and 104,926 were recognized as ORFs (57.27%). In addition, 79,185 transcripts were predicted to exist with at least one hit to the Pfam database. A number of 3,931 transcription factors were identified by BLAST searching against PlnTFDB. Furthermore, 6,591 of the predicted peptide sequences contained signaling peptides, while 92,704 contained transmembrane domains. Comparison of the assembled transcripts with transcripts of the walnut and published genome assembly for the 'Chandler' cultivar using the BLAST algorithm led to identify a total number of 27,304 and 19,178 homologue transcripts, respectively. De novo transcriptomes in walnut leaves can be developed for the future studies in functional genomics and genetic studies of walnuts. |
| doi_str_mv | 10.1371/journal.pone.0232005 |
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Finding the best transcriptome assembly has not been the subject of walnuts research as yet. This research generated 240,179,782 reads from 11 walnut leaves according to cDNA libraries. The reads provided a complete de novo transcriptome assembly. Fifteen different transcriptome assemblies were constructed from five different well-known assemblers used in scientific literature with different k-mer lengths (Bridger, BinPacker, SOAPdenovo-Trans, Trinity and SPAdes) as well as two merging approaches (EvidentialGene and Transfuse). Based on the four quality metrics of assembly, the results indicated an efficiency in the process of merging the assemblies after being generated by de novo assemblers. Finally, EvidentialGene was recognized as the best assembler for the de novo assembly of the leaf transcriptome in walnut. Among a total number of 183,191 transcripts which were generated by EvidentialGene, there were 109,413 transcripts capable of protein potential (59.72%) and 104,926 were recognized as ORFs (57.27%). In addition, 79,185 transcripts were predicted to exist with at least one hit to the Pfam database. A number of 3,931 transcription factors were identified by BLAST searching against PlnTFDB. Furthermore, 6,591 of the predicted peptide sequences contained signaling peptides, while 92,704 contained transmembrane domains. Comparison of the assembled transcripts with transcripts of the walnut and published genome assembly for the 'Chandler' cultivar using the BLAST algorithm led to identify a total number of 27,304 and 19,178 homologue transcripts, respectively. De novo transcriptomes in walnut leaves can be developed for the future studies in functional genomics and genetic studies of walnuts.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0232005</identifier><identifier>PMID: 32343733</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Analysis ; Arthropods ; Assemblies ; Assembly ; Biology and Life Sciences ; Computational Biology - methods ; Contig Mapping - methods ; Crop yields ; Cultivars ; DNA binding proteins ; Explosions ; Future predictions ; Gene expression ; Gene Expression Profiling - methods ; Gene Library ; Genomes ; Genomic libraries ; Genomics ; High-Throughput Nucleotide Sequencing - methods ; Homology ; Horticulture ; Juglans - genetics ; Leaves ; Molecular Sequence Annotation ; Peptides ; Plant Leaves - genetics ; Plant Proteins - genetics ; Research and Analysis Methods ; Researchers ; Science literature ; Sequence Analysis, RNA - methods ; Soil sciences ; Studies ; Transcription factors ; Transmembrane domains ; Walnuts</subject><ispartof>PloS one, 2020-04, Vol.15 (4), p.e0232005-e0232005</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Sadat-Hosseini et al. 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Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Sadat-Hosseini et al 2020 Sadat-Hosseini et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-d6ecc9e8a60e2b19b38df72c381a66a32d54e874c6008b8e6ebf274602235bb03</citedby><cites>FETCH-LOGICAL-c692t-d6ecc9e8a60e2b19b38df72c381a66a32d54e874c6008b8e6ebf274602235bb03</cites><orcidid>0000-0001-8458-8697</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188282/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188282/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32343733$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kumar, Shailesh</contributor><creatorcontrib>Sadat-Hosseini, Mohammad</creatorcontrib><creatorcontrib>Bakhtiarizadeh, Mohammad Reza</creatorcontrib><creatorcontrib>Boroomand, Naser</creatorcontrib><creatorcontrib>Tohidfar, Masoud</creatorcontrib><creatorcontrib>Vahdati, Kourosh</creatorcontrib><title>Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Transcriptome resources can facilitate to increase yield and quality of walnuts. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sadat-Hosseini, Mohammad</au><au>Bakhtiarizadeh, Mohammad Reza</au><au>Boroomand, Naser</au><au>Tohidfar, Masoud</au><au>Vahdati, Kourosh</au><au>Kumar, Shailesh</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-04-28</date><risdate>2020</risdate><volume>15</volume><issue>4</issue><spage>e0232005</spage><epage>e0232005</epage><pages>e0232005-e0232005</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Transcriptome resources can facilitate to increase yield and quality of walnuts. Finding the best transcriptome assembly has not been the subject of walnuts research as yet. This research generated 240,179,782 reads from 11 walnut leaves according to cDNA libraries. The reads provided a complete de novo transcriptome assembly. Fifteen different transcriptome assemblies were constructed from five different well-known assemblers used in scientific literature with different k-mer lengths (Bridger, BinPacker, SOAPdenovo-Trans, Trinity and SPAdes) as well as two merging approaches (EvidentialGene and Transfuse). Based on the four quality metrics of assembly, the results indicated an efficiency in the process of merging the assemblies after being generated by de novo assemblers. Finally, EvidentialGene was recognized as the best assembler for the de novo assembly of the leaf transcriptome in walnut. Among a total number of 183,191 transcripts which were generated by EvidentialGene, there were 109,413 transcripts capable of protein potential (59.72%) and 104,926 were recognized as ORFs (57.27%). In addition, 79,185 transcripts were predicted to exist with at least one hit to the Pfam database. A number of 3,931 transcription factors were identified by BLAST searching against PlnTFDB. Furthermore, 6,591 of the predicted peptide sequences contained signaling peptides, while 92,704 contained transmembrane domains. Comparison of the assembled transcripts with transcripts of the walnut and published genome assembly for the 'Chandler' cultivar using the BLAST algorithm led to identify a total number of 27,304 and 19,178 homologue transcripts, respectively. De novo transcriptomes in walnut leaves can be developed for the future studies in functional genomics and genetic studies of walnuts.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32343733</pmid><doi>10.1371/journal.pone.0232005</doi><orcidid>https://orcid.org/0000-0001-8458-8697</orcidid><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Analysis Arthropods Assemblies Assembly Biology and Life Sciences Computational Biology - methods Contig Mapping - methods Crop yields Cultivars DNA binding proteins Explosions Future predictions Gene expression Gene Expression Profiling - methods Gene Library Genomes Genomic libraries Genomics High-Throughput Nucleotide Sequencing - methods Homology Horticulture Juglans - genetics Leaves Molecular Sequence Annotation Peptides Plant Leaves - genetics Plant Proteins - genetics Research and Analysis Methods Researchers Science literature Sequence Analysis, RNA - methods Soil sciences Studies Transcription factors Transmembrane domains Walnuts |
| title | Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T04%3A17%3A16IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Combining%20independent%20de%20novo%20assemblies%20to%20optimize%20leaf%20transcriptome%20of%20Persian%20walnut&rft.jtitle=PloS%20one&rft.au=Sadat-Hosseini,%20Mohammad&rft.date=2020-04-28&rft.volume=15&rft.issue=4&rft.spage=e0232005&rft.epage=e0232005&rft.pages=e0232005-e0232005&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0232005&rft_dat=%3Cgale_plos_%3EA622217971%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2395605835&rft_id=info:pmid/32343733&rft_galeid=A622217971&rft_doaj_id=oai_doaj_org_article_2c0b83e449984da0a669d1ff11ddbe29&rfr_iscdi=true |