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, 8 (3), 133

Enrichment of Genomic Resources and Identification of Simple Sequence Repeats From Medicinally Important Clausena excavata

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Enrichment of Genomic Resources and Identification of Simple Sequence Repeats From Medicinally Important Clausena excavata

Doo Young Bae et al. 3 Biotech.

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.

Keywords: Clausena species; Medicinal plant; RNA-seq; SSR marker.

Conflict of interest statement

Compliance with ethical standardsThe authors declare that they have no conflict of interests.

Figures

Fig. 1
Fig. 1
Length distribution of unigenes from the RNA-seq of C. excavata
Fig. 2
Fig. 2
Top species with high hits of unigenes from the RNA-seq of C. excavata
Fig. 3
Fig. 3
Gene ontology term distribution of RNA-seq unigenes. Numbers at the end of each bar denote numbers of unigenes involved in the given process
Fig. 4
Fig. 4
UPGMA dendrogram using the genic regions from the five Clausena and two Citrus species. The dendrogram was reconstructed by the UPGMA method based on genic regions amplified from the five Clausena species using three SSR primers. Two Citrus species were used as the outgroup and their corresponding sequences (XP_006477474.1: Endoplasmic reticulum membrane protein-like; XP_006476478.1: Reticulon-like protein B2, and XP_006487028.1: Protein IRX15-LIKE-like) were retrieved from the NCBI database. Tree was shown with the percentage of replicate trees with 1000 bootstrap replications

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