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Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing
The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691156/ https://www.ncbi.nlm.nih.gov/pubmed/26694362 http://dx.doi.org/10.3390/ijms161226213 |
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author | Patnaik, Bharat Bhusan Hwang, Hee-Ju Kang, Se Won Park, So Young Wang, Tae Hun Park, Eun Bi Chung, Jong Min Song, Dae Kwon Kim, Changmu Kim, Soonok Lee, Jae Bong Jeong, Heon Cheon Park, Hong Seog Han, Yeon Soo Lee, Yong Seok |
author_facet | Patnaik, Bharat Bhusan Hwang, Hee-Ju Kang, Se Won Park, So Young Wang, Tae Hun Park, Eun Bi Chung, Jong Min Song, Dae Kwon Kim, Changmu Kim, Soonok Lee, Jae Bong Jeong, Heon Cheon Park, Hong Seog Han, Yeon Soo Lee, Yong Seok |
author_sort | Patnaik, Bharat Bhusan |
collection | PubMed |
description | The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10(−5)) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species. |
format | Online Article Text |
id | pubmed-4691156 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-46911562016-01-06 Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing Patnaik, Bharat Bhusan Hwang, Hee-Ju Kang, Se Won Park, So Young Wang, Tae Hun Park, Eun Bi Chung, Jong Min Song, Dae Kwon Kim, Changmu Kim, Soonok Lee, Jae Bong Jeong, Heon Cheon Park, Hong Seog Han, Yeon Soo Lee, Yong Seok Int J Mol Sci Article The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10(−5)) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species. MDPI 2015-12-16 /pmc/articles/PMC4691156/ /pubmed/26694362 http://dx.doi.org/10.3390/ijms161226213 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Patnaik, Bharat Bhusan Hwang, Hee-Ju Kang, Se Won Park, So Young Wang, Tae Hun Park, Eun Bi Chung, Jong Min Song, Dae Kwon Kim, Changmu Kim, Soonok Lee, Jae Bong Jeong, Heon Cheon Park, Hong Seog Han, Yeon Soo Lee, Yong Seok Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title | Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title_full | Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title_fullStr | Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title_full_unstemmed | Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title_short | Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing |
title_sort | transcriptome characterization for non-model endangered lycaenids, protantigius superans and spindasis takanosis, using illumina hiseq 2500 sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691156/ https://www.ncbi.nlm.nih.gov/pubmed/26694362 http://dx.doi.org/10.3390/ijms161226213 |
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