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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Veröffentlicht in:3 Biotech 2018-03, Vol.8 (3), p.133-133, Article 133
Hauptverfasser: 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
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container_end_page 133
container_issue 3
container_start_page 133
container_title 3 Biotech
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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.
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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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