RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862. Issue 2 (17th February 2016)

• Record Type: Journal Article
• Authors: Hwang, Hee‐Ju; Patnaik, Bharat Bhusan; Kang, Se Won; Park, So Young; Wang, Tae Hun; Park, Eun Bi; Chung, Jong Min; Song, Dae Kwon; Patnaik, Hongray Howrelia; Kim, Changmu; Kim, Soonok; Lee, Jae Bong; Jeong, Heon Cheon; Park, Hong Seog; Han, Yeon Soo; Lee, Yong Seok
• Is Part Of: Entomological research. Volume 46:Issue 2(2016:Mar.)
• Page Start: 148
• Page End: 161
• Publication Date: 2016-02-17
• Subjects: butterflies -- endangered species -- Fabriciana nerippe -- RNA sequencing -- SSR; Insects -- Korea -- Periodicals; Entomology -- Periodicals; 595.709519
• DOI: 10.1111/1748-5967.12164
• Languages: English
• ISSNs: 1738-2297

Abstract

Abstract: Grassland butterflies are considered representative indicators of biodiversity and ecosystem health. Their dramatic decline caused by habitat destruction, intensifying agriculture and global warming has prompted concern for conservation. While ecological indices of butterflies have been documented, there is a lack of genomic resources relative to the biological importance of this group. Here, we report, first whole‐transcriptomic resource for F abriciana nerippe, a brush‐footed butterfly member that is endangered in Korea. Approximately, 241.3 million clean reads were obtained from paired‐end Illumina sequencing of adult whole‐body RNA. The de novo assembly resulted in 114 405 unigenes with length ranging from 133 to 33 218 bp. We found 41 868 assembled unigenes homologous to sequences in locally curated PANM‐DB (Protostome DB). We assigned gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology terms to 18 085 and 5779 unigenes, respectively. InterProScan predicted 6691 protein domains for the assembled unigene sequences, with the reverse transcriptase and zinc finger domains found to be the most predominant. A total of 315 282 simple sequence repeats (SSRs) were identified from the assembled unigenes, when considering dinucleotide to octanucleotide repeats with a minimum of three repeat units. AT/AT, AAT/ATT, and AAAT/ATTT represented the most prominent SSR repeat types in the transcriptome. The unigene annotation profile and microsatellites generated in the study can serve as a reference resource for closely related species and gene functional analysis studies. Our data can be utilized to study ecological drift and loss of the species, consequently leading to better protection of the population.