De novo assembly and annotation of the juvenile tuber transcriptome of agastrodia elatahybrid by rna sequencing: Detection of ssr markers

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dc.authorid0000-0002-7470-0080en_US
dc.authorid0000-0002-0595-5661en_US
dc.contributor.authorWang, Yunsheng
dc.contributor.authorShahid, Muhammad Qasim
dc.contributor.authorGhouri, Fozia
dc.contributor.authorBaloch, Faheem Shehzad
dc.date.accessioned2021-06-23T19:54:04Z
dc.date.available2021-06-23T19:54:04Z
dc.date.issued2020
dc.departmentBAİBÜ, Ziraat Fakültesi, Tarla Bitkileri Bölümüen_US
dc.description.abstractGastrodia elatais a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of aG. elatahybrid (Gastrodia elata BI.f.elata x Gastrodia elata BI.f.pilifera) by using Illumina HiSeq (TM) 4000 sequencing platform. De novo assembly and bioinformatics analysis revealed 20,237,474 clean reads, including 2,529,684,250 bp that assembled into 34,323 unigenes with an average length of 695.19 bp. Among them, 24,698 (71.96%) unigenes were annotated by at least one of the Nr, Swiss-Prot, COG and KEGG databases. A total of 4236 (12.34%) unigenes were identified as candidate transcription factors, and 2007 (5.85%) unigenes were found to contain at least one single sequence repeat (SSR). Of these SSRs, AG/CT repeat motif was the most frequent, with a total of 498 (21.67%). This study will enhance our understanding about the molecular mechanism of physiological metabolism, growth and development ofG. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.en_US
dc.identifier.doi10.1007/s10528-020-09983-w
dc.identifier.endpage934en_US
dc.identifier.issn0006-2928
dc.identifier.issn1573-4927
dc.identifier.issue6en_US
dc.identifier.pmid32632662en_US
dc.identifier.scopus2-s2.0-85087486517en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage914en_US
dc.identifier.urihttps://doi.org/10.1007/s10528-020-09983-w
dc.identifier.urihttps://hdl.handle.net/20.500.12491/10404
dc.identifier.volume58en_US
dc.identifier.wosWOS:000545899500001en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorBaloch, Faheem Shehzad
dc.language.isoenen_US
dc.publisherSpringer/Plenum Publishersen_US
dc.relation.ispartofBiochemical Geneticsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectGastrodia elataen_US
dc.subjectSequencingen_US
dc.subjectSSRen_US
dc.subjectTranscriptomeen_US
dc.subjectUnigenesen_US
dc.titleDe novo assembly and annotation of the juvenile tuber transcriptome of agastrodia elatahybrid by rna sequencing: Detection of ssr markersen_US
dc.typeArticleen_US

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