Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1)
Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of thre...
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| creator | Wei, Fu-Jin Ueno, Saneyoshi Ujino-Ihara, Tokuko Saito, Maki Tsumura, Yoshihiko Higuchi, Yuumi Hirayama, Satoko Iwai, Junji Hakamata, Tetsuji Moriguchi, Yoshinari |
| description | Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. Compared to other full-length cDNA resources collected by Sanger and PacBio sequencers, the extent of the coverage in our dataset was the highest, indicating that these data can be safely used for further studies. When two tissue-specific libraries were compared, there were significant expression differences between male strobili and leaf and bark sets. Moreover, subtle expression difference between male-fertile and sterile libraries were detected. Orthologous genes from other model plants and conifer species were identified. We demonstrated that our transcriptome assembly output (CJ3006NRE) can serve as a reference transcriptome for future functional genomics and evolutionary biology studies. |
| doi_str_mv | 10.1371/journal.pone.0247180 |
| format | Article |
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Don) focusing on MALE STERILITY 1 (MS1)</title><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>Public Library of Science (PLoS)</source><creator>Wei, Fu-Jin ; Ueno, Saneyoshi ; Ujino-Ihara, Tokuko ; Saito, Maki ; Tsumura, Yoshihiko ; Higuchi, Yuumi ; Hirayama, Satoko ; Iwai, Junji ; Hakamata, Tetsuji ; Moriguchi, Yoshinari</creator><creatorcontrib>Wei, Fu-Jin ; Ueno, Saneyoshi ; Ujino-Ihara, Tokuko ; Saito, Maki ; Tsumura, Yoshihiko ; Higuchi, Yuumi ; Hirayama, Satoko ; Iwai, Junji ; Hakamata, Tetsuji ; Moriguchi, Yoshinari</creatorcontrib><description>Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. Compared to other full-length cDNA resources collected by Sanger and PacBio sequencers, the extent of the coverage in our dataset was the highest, indicating that these data can be safely used for further studies. When two tissue-specific libraries were compared, there were significant expression differences between male strobili and leaf and bark sets. Moreover, subtle expression difference between male-fertile and sterile libraries were detected. Orthologous genes from other model plants and conifer species were identified. We demonstrated that our transcriptome assembly output (CJ3006NRE) can serve as a reference transcriptome for future functional genomics and evolutionary biology studies.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0247180</identifier><identifier>PMID: 33630910</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Afforestation ; Assembly ; Bark ; Biology and Life Sciences ; Conifers ; Contamination ; Cryptomeria japonica ; Developmental biology ; Forest products ; Forestry ; Gene expression ; Genes ; Genetic engineering ; Genomes ; Genomics ; Libraries ; Male sterility ; Males ; Open source software ; Proteins ; Quality control ; Research and analysis methods ; Transcriptomes ; Transcriptomics ; Trees ; Workflow</subject><ispartof>PloS one, 2021-02, Vol.16 (2), p.e0247180-e0247180</ispartof><rights>2021 Wei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Wei et al 2021 Wei et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c570t-be5c00ccbdf046e91a9a3945c9b08f7b77b90dad853d363c37ba4ee94be31db63</citedby><cites>FETCH-LOGICAL-c570t-be5c00ccbdf046e91a9a3945c9b08f7b77b90dad853d363c37ba4ee94be31db63</cites><orcidid>0000-0001-5571-0622</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/PMC7935350/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935350/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33630910$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wei, Fu-Jin</creatorcontrib><creatorcontrib>Ueno, Saneyoshi</creatorcontrib><creatorcontrib>Ujino-Ihara, Tokuko</creatorcontrib><creatorcontrib>Saito, Maki</creatorcontrib><creatorcontrib>Tsumura, Yoshihiko</creatorcontrib><creatorcontrib>Higuchi, Yuumi</creatorcontrib><creatorcontrib>Hirayama, Satoko</creatorcontrib><creatorcontrib>Iwai, Junji</creatorcontrib><creatorcontrib>Hakamata, Tetsuji</creatorcontrib><creatorcontrib>Moriguchi, Yoshinari</creatorcontrib><title>Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. 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| subjects | Afforestation Assembly Bark Biology and Life Sciences Conifers Contamination Cryptomeria japonica Developmental biology Forest products Forestry Gene expression Genes Genetic engineering Genomes Genomics Libraries Male sterility Males Open source software Proteins Quality control Research and analysis methods Transcriptomes Transcriptomics Trees Workflow |
| title | Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1) |
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