Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea
RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Curr...
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Veröffentlicht in: | Genes 2023-04, Vol.14 (5), p.989 |
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description | RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237
RNA-seq runs and assembled a transcriptome with 84,827 sequences from 49,320 genes, identifying 64,582 mRNA from 35,485 genes, 20,217 lncRNA from 17,084 genes, and 3481 circRNAs from 1103 genes. In addition, we performed a co-expression analysis of lncRNA and mRNA and identified that 1319 lncRNA co-express with at least one mRNA. Further analysis of samples from
sexual and asexual strains revealed the role of sexual reproduction in gene expression profiles. Samples from different parts of asexual
revealed that differential expression profiles of different body parts correlated with the function of conduction of nerve impulses. In conclusion, PipeOne-NM has the potential to provide comprehensive transcriptome information for non-model organisms on a single platform. |
doi_str_mv | 10.3390/genes14050989 |
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RNA-seq runs and assembled a transcriptome with 84,827 sequences from 49,320 genes, identifying 64,582 mRNA from 35,485 genes, 20,217 lncRNA from 17,084 genes, and 3481 circRNAs from 1103 genes. In addition, we performed a co-expression analysis of lncRNA and mRNA and identified that 1319 lncRNA co-express with at least one mRNA. Further analysis of samples from
sexual and asexual strains revealed the role of sexual reproduction in gene expression profiles. Samples from different parts of asexual
revealed that differential expression profiles of different body parts correlated with the function of conduction of nerve impulses. In conclusion, PipeOne-NM has the potential to provide comprehensive transcriptome information for non-model organisms on a single platform.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes14050989</identifier><identifier>PMID: 37239350</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Alternative splicing ; Annotations ; Biology ; Data collection ; Gene expression ; Genomes ; Mediterranea ; MicroRNAs ; Non-coding RNA ; Proteins ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; RNA-Seq ; Schmidtea mediterranea ; Sequence Analysis, RNA ; Sexual reproduction ; Transcriptomes</subject><ispartof>Genes, 2023-04, Vol.14 (5), p.989</ispartof><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c372t-228e2584c57dda2629f44ed91445589b34b2ce5b4e6463bc1e0bdb03120d5d7c3</cites><orcidid>0000-0002-3227-5215</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/PMC10218480/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218480/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37239350$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Yanzhi</creatorcontrib><creatorcontrib>Li, Sijun</creatorcontrib><creatorcontrib>Nong, Baoting</creatorcontrib><creatorcontrib>Zhou, Weiping</creatorcontrib><creatorcontrib>Xu, Shuhua</creatorcontrib><creatorcontrib>Songyang, Zhou</creatorcontrib><creatorcontrib>Xiong, Yuanyan</creatorcontrib><title>Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237
RNA-seq runs and assembled a transcriptome with 84,827 sequences from 49,320 genes, identifying 64,582 mRNA from 35,485 genes, 20,217 lncRNA from 17,084 genes, and 3481 circRNAs from 1103 genes. In addition, we performed a co-expression analysis of lncRNA and mRNA and identified that 1319 lncRNA co-express with at least one mRNA. Further analysis of samples from
sexual and asexual strains revealed the role of sexual reproduction in gene expression profiles. Samples from different parts of asexual
revealed that differential expression profiles of different body parts correlated with the function of conduction of nerve impulses. In conclusion, PipeOne-NM has the potential to provide comprehensive transcriptome information for non-model organisms on a single platform.</description><subject>Alternative splicing</subject><subject>Annotations</subject><subject>Biology</subject><subject>Data collection</subject><subject>Gene expression</subject><subject>Genomes</subject><subject>Mediterranea</subject><subject>MicroRNAs</subject><subject>Non-coding RNA</subject><subject>Proteins</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Messenger - genetics</subject><subject>RNA-Seq</subject><subject>Schmidtea mediterranea</subject><subject>Sequence Analysis, RNA</subject><subject>Sexual reproduction</subject><subject>Transcriptomes</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkUlLBDEQhYMoKurRqwS8eGnNOtM5yTC4gRsu55BOamYi3Umb9Az47424oOZSgfp49aoeQvuUHHOuyMkcAmQqiCSqVmtom5Exr4Rgcv3Xfwvt5fxCyhOEESI30RYfM664JNuom8auT7CAkP0K8MPtpHqEVzwJpn3LPuN730PrA-BZTPg2huomOmjxXZqb4HOXsQkOXw0ZT_q-9dYMPgbsA360i867AQzuwPkBUjIBzC7amJk2w95X3UHP52dP08vq-u7iajq5rmxxNlSM1cBkLawcO2fYiKmZEOAUFULKWjVcNMyCbASMxIg3lgJpXEM4ZcRJN7Z8B51-6vbLpsy3EIZkWt0n35n0pqPx-m8n-IWex5WmhNFa1KQoHH0ppPi6hDzozmcLbVvWiMusWV1OyYohUdDDf-hLXKZywA-KKiFqqVihqk_KpphzgtmPG0r0R5j6T5iFP_i9wg_9HR1_B6Uom2w</recordid><startdate>20230427</startdate><enddate>20230427</enddate><creator>Wang, Yanzhi</creator><creator>Li, Sijun</creator><creator>Nong, Baoting</creator><creator>Zhou, Weiping</creator><creator>Xu, Shuhua</creator><creator>Songyang, Zhou</creator><creator>Xiong, Yuanyan</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-3227-5215</orcidid></search><sort><creationdate>20230427</creationdate><title>Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea</title><author>Wang, Yanzhi ; Li, Sijun ; Nong, Baoting ; Zhou, Weiping ; Xu, Shuhua ; Songyang, Zhou ; Xiong, Yuanyan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-228e2584c57dda2629f44ed91445589b34b2ce5b4e6463bc1e0bdb03120d5d7c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Alternative splicing</topic><topic>Annotations</topic><topic>Biology</topic><topic>Data collection</topic><topic>Gene expression</topic><topic>Genomes</topic><topic>Mediterranea</topic><topic>MicroRNAs</topic><topic>Non-coding RNA</topic><topic>Proteins</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Messenger - genetics</topic><topic>RNA-Seq</topic><topic>Schmidtea mediterranea</topic><topic>Sequence Analysis, RNA</topic><topic>Sexual reproduction</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Yanzhi</creatorcontrib><creatorcontrib>Li, Sijun</creatorcontrib><creatorcontrib>Nong, Baoting</creatorcontrib><creatorcontrib>Zhou, Weiping</creatorcontrib><creatorcontrib>Xu, Shuhua</creatorcontrib><creatorcontrib>Songyang, Zhou</creatorcontrib><creatorcontrib>Xiong, Yuanyan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Yanzhi</au><au>Li, Sijun</au><au>Nong, Baoting</au><au>Zhou, Weiping</au><au>Xu, Shuhua</au><au>Songyang, Zhou</au><au>Xiong, Yuanyan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2023-04-27</date><risdate>2023</risdate><volume>14</volume><issue>5</issue><spage>989</spage><pages>989-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237
RNA-seq runs and assembled a transcriptome with 84,827 sequences from 49,320 genes, identifying 64,582 mRNA from 35,485 genes, 20,217 lncRNA from 17,084 genes, and 3481 circRNAs from 1103 genes. In addition, we performed a co-expression analysis of lncRNA and mRNA and identified that 1319 lncRNA co-express with at least one mRNA. Further analysis of samples from
sexual and asexual strains revealed the role of sexual reproduction in gene expression profiles. Samples from different parts of asexual
revealed that differential expression profiles of different body parts correlated with the function of conduction of nerve impulses. In conclusion, PipeOne-NM has the potential to provide comprehensive transcriptome information for non-model organisms on a single platform.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>37239350</pmid><doi>10.3390/genes14050989</doi><orcidid>https://orcid.org/0000-0002-3227-5215</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Alternative splicing Annotations Biology Data collection Gene expression Genomes Mediterranea MicroRNAs Non-coding RNA Proteins RNA, Long Noncoding - genetics RNA, Messenger - genetics RNA-Seq Schmidtea mediterranea Sequence Analysis, RNA Sexual reproduction Transcriptomes |
title | Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea |
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