Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata
To broaden and delve into the genomic information of Clausena excavata , an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly f...
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creator | Bae, Doo Young Eum, Sang Mi Lee, Sang Woo Paik, Jin-Hyub Kim, Soo-Yong Park, Mihyun Lee, Changyoung Tran, The Bach Do, Van Hai Heo, Jae-Yun Seong, Eun-Soo Kim, Il-Seop Choi, Ki-Young Hong, Jin Sung Ramekar, Rahul Vasudeo Choi, Sangho Na, Jong-Kuk |
description | To broaden and delve into the genomic information of
Clausena excavata
, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five
Clausena
species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of
Clausena
species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000. |
doi_str_mv | 10.1007/s13205-018-1162-x |
format | Article |
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Clausena excavata
, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five
Clausena
species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of
Clausena
species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.</description><identifier>ISSN: 2190-572X</identifier><identifier>EISSN: 2190-5738</identifier><identifier>DOI: 10.1007/s13205-018-1162-x</identifier><identifier>PMID: 29479509</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agriculture ; Asia ; Assembly ; biochemical pathways ; Bioinformatics ; Biological activity ; Biomaterials ; Biotechnology ; Cancer Research ; Chemistry ; Chemistry and Materials Science ; Clausena ; Encyclopedias ; Gene expression ; gene ontology ; Gene polymorphism ; Gene sequencing ; Genes ; Genomes ; genomics ; Medicinal plants ; Metabolic pathways ; Metabolism ; microsatellite repeats ; Original ; Original Article ; Polymorphism ; Ribonucleic acid ; RNA ; sequence analysis ; Simple sequence repeats ; Stem Cells ; transcriptome ; unigenes</subject><ispartof>3 Biotech, 2018-03, Vol.8 (3), p.133-133, Article 133</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2018</rights><rights>3 Biotech is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c503t-9e1edc5fda2ebf53446c45d8af7f3ba5ac605abc880f955cf5da592bd5f37843</citedby><cites>FETCH-LOGICAL-c503t-9e1edc5fda2ebf53446c45d8af7f3ba5ac605abc880f955cf5da592bd5f37843</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814389/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814389/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,41464,42533,51294,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29479509$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bae, Doo Young</creatorcontrib><creatorcontrib>Eum, Sang Mi</creatorcontrib><creatorcontrib>Lee, Sang Woo</creatorcontrib><creatorcontrib>Paik, Jin-Hyub</creatorcontrib><creatorcontrib>Kim, Soo-Yong</creatorcontrib><creatorcontrib>Park, Mihyun</creatorcontrib><creatorcontrib>Lee, Changyoung</creatorcontrib><creatorcontrib>Tran, The Bach</creatorcontrib><creatorcontrib>Do, Van Hai</creatorcontrib><creatorcontrib>Heo, Jae-Yun</creatorcontrib><creatorcontrib>Seong, Eun-Soo</creatorcontrib><creatorcontrib>Kim, Il-Seop</creatorcontrib><creatorcontrib>Choi, Ki-Young</creatorcontrib><creatorcontrib>Hong, Jin Sung</creatorcontrib><creatorcontrib>Ramekar, Rahul Vasudeo</creatorcontrib><creatorcontrib>Choi, Sangho</creatorcontrib><creatorcontrib>Na, Jong-Kuk</creatorcontrib><title>Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata</title><title>3 Biotech</title><addtitle>3 Biotech</addtitle><addtitle>3 Biotech</addtitle><description>To broaden and delve into the genomic information of
Clausena excavata
, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five
Clausena
species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of
Clausena
species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.</description><subject>Agriculture</subject><subject>Asia</subject><subject>Assembly</subject><subject>biochemical pathways</subject><subject>Bioinformatics</subject><subject>Biological activity</subject><subject>Biomaterials</subject><subject>Biotechnology</subject><subject>Cancer Research</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Clausena</subject><subject>Encyclopedias</subject><subject>Gene expression</subject><subject>gene ontology</subject><subject>Gene polymorphism</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>genomics</subject><subject>Medicinal plants</subject><subject>Metabolic pathways</subject><subject>Metabolism</subject><subject>microsatellite repeats</subject><subject>Original</subject><subject>Original Article</subject><subject>Polymorphism</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>sequence analysis</subject><subject>Simple sequence repeats</subject><subject>Stem Cells</subject><subject>transcriptome</subject><subject>unigenes</subject><issn>2190-572X</issn><issn>2190-5738</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNqNkkuLFDEUhYMoztDOD3AjATduSvOodCUbQZrxAQNuZuEu3Erd9GSoStqkaujx15u2x_YBgtkkcL-c3HNzCHnO2WvOWPemcCmYahjXDedr0ewfkXPBDWtUJ_Xj01l8OSMXpdyyuhRXhrOn5EyYtjOKmXPy7TLm4G4mjDNNnm4xpik4mrGkJTssFOJAw1DLwQcHc0jxwJUw7UakBb8uGB1WfocwF-pzmuiEQ3Ahwjje08qlPENV34ywFIxAce_gDmZ4Rp54GAtePOwrcv3-8nrzsbn6_OHT5t1V4xSTc2OQ4-CUH0Bg75Vs27Vr1aDBd172oMCtmYLeac28Ucp5NYAyoh-Ul51u5Yq8Pcrulr525qqVDKPd5TBBvrcJgv2zEsON3aY7qzRvpTZV4NWDQE7VbpntFIrDcYSIaSlWsLaivDXdf6BMyzVv17qiL_9Cb-vE69B-UEIaI6r9FeFHyuVUSkZ_6psze4iBPcbA1hjYQwzsvt558bvh042fn14BcQRKLcUt5l9P_1v1Ox8pwdk</recordid><startdate>20180301</startdate><enddate>20180301</enddate><creator>Bae, Doo Young</creator><creator>Eum, Sang Mi</creator><creator>Lee, Sang Woo</creator><creator>Paik, Jin-Hyub</creator><creator>Kim, Soo-Yong</creator><creator>Park, Mihyun</creator><creator>Lee, Changyoung</creator><creator>Tran, The Bach</creator><creator>Do, Van Hai</creator><creator>Heo, Jae-Yun</creator><creator>Seong, Eun-Soo</creator><creator>Kim, Il-Seop</creator><creator>Choi, Ki-Young</creator><creator>Hong, Jin Sung</creator><creator>Ramekar, Rahul Vasudeo</creator><creator>Choi, Sangho</creator><creator>Na, Jong-Kuk</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8AO</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>ABJCF</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>LK8</scope><scope>M7P</scope><scope>M7S</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20180301</creationdate><title>Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata</title><author>Bae, Doo Young ; Eum, Sang Mi ; Lee, Sang Woo ; Paik, Jin-Hyub ; Kim, Soo-Yong ; Park, Mihyun ; Lee, Changyoung ; Tran, The Bach ; Do, Van Hai ; Heo, Jae-Yun ; Seong, Eun-Soo ; Kim, Il-Seop ; Choi, Ki-Young ; Hong, Jin Sung ; Ramekar, Rahul Vasudeo ; Choi, Sangho ; Na, Jong-Kuk</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c503t-9e1edc5fda2ebf53446c45d8af7f3ba5ac605abc880f955cf5da592bd5f37843</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Agriculture</topic><topic>Asia</topic><topic>Assembly</topic><topic>biochemical pathways</topic><topic>Bioinformatics</topic><topic>Biological activity</topic><topic>Biomaterials</topic><topic>Biotechnology</topic><topic>Cancer Research</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Clausena</topic><topic>Encyclopedias</topic><topic>Gene expression</topic><topic>gene ontology</topic><topic>Gene polymorphism</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>genomics</topic><topic>Medicinal plants</topic><topic>Metabolic pathways</topic><topic>Metabolism</topic><topic>microsatellite repeats</topic><topic>Original</topic><topic>Original Article</topic><topic>Polymorphism</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>sequence analysis</topic><topic>Simple sequence repeats</topic><topic>Stem Cells</topic><topic>transcriptome</topic><topic>unigenes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bae, Doo Young</creatorcontrib><creatorcontrib>Eum, Sang Mi</creatorcontrib><creatorcontrib>Lee, Sang Woo</creatorcontrib><creatorcontrib>Paik, Jin-Hyub</creatorcontrib><creatorcontrib>Kim, Soo-Yong</creatorcontrib><creatorcontrib>Park, Mihyun</creatorcontrib><creatorcontrib>Lee, Changyoung</creatorcontrib><creatorcontrib>Tran, The Bach</creatorcontrib><creatorcontrib>Do, Van Hai</creatorcontrib><creatorcontrib>Heo, Jae-Yun</creatorcontrib><creatorcontrib>Seong, Eun-Soo</creatorcontrib><creatorcontrib>Kim, Il-Seop</creatorcontrib><creatorcontrib>Choi, Ki-Young</creatorcontrib><creatorcontrib>Hong, Jin Sung</creatorcontrib><creatorcontrib>Ramekar, Rahul Vasudeo</creatorcontrib><creatorcontrib>Choi, Sangho</creatorcontrib><creatorcontrib>Na, Jong-Kuk</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Engineering 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>Engineering Collection</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>3 Biotech</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bae, Doo Young</au><au>Eum, Sang Mi</au><au>Lee, Sang Woo</au><au>Paik, Jin-Hyub</au><au>Kim, Soo-Yong</au><au>Park, Mihyun</au><au>Lee, Changyoung</au><au>Tran, The Bach</au><au>Do, Van Hai</au><au>Heo, Jae-Yun</au><au>Seong, Eun-Soo</au><au>Kim, Il-Seop</au><au>Choi, Ki-Young</au><au>Hong, Jin Sung</au><au>Ramekar, Rahul Vasudeo</au><au>Choi, Sangho</au><au>Na, Jong-Kuk</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata</atitle><jtitle>3 Biotech</jtitle><stitle>3 Biotech</stitle><addtitle>3 Biotech</addtitle><date>2018-03-01</date><risdate>2018</risdate><volume>8</volume><issue>3</issue><spage>133</spage><epage>133</epage><pages>133-133</pages><artnum>133</artnum><issn>2190-572X</issn><eissn>2190-5738</eissn><abstract>To broaden and delve into the genomic information of
Clausena excavata
, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five
Clausena
species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of
Clausena
species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>29479509</pmid><doi>10.1007/s13205-018-1162-x</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Agriculture Asia Assembly biochemical pathways Bioinformatics Biological activity Biomaterials Biotechnology Cancer Research Chemistry Chemistry and Materials Science Clausena Encyclopedias Gene expression gene ontology Gene polymorphism Gene sequencing Genes Genomes genomics Medicinal plants Metabolic pathways Metabolism microsatellite repeats Original Original Article Polymorphism Ribonucleic acid RNA sequence analysis Simple sequence repeats Stem Cells transcriptome unigenes |
title | Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata |
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