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Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery
An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this specie...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962005/ https://www.ncbi.nlm.nih.gov/pubmed/27455329 http://dx.doi.org/10.3390/genes7070035 |
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author | Park, So Young Patnaik, Bharat Bhusan Kang, Se Won Hwang, Hee-Ju Chung, Jong Min Song, Dae Kwon Sang, Min Kyu Patnaik, Hongray Howrelia Lee, Jae Bong Noh, Mi Young Kim, Changmu Kim, Soonok Park, Hong Seog Lee, Jun Sang Han, Yeon Soo Lee, Yong Seok |
author_facet | Park, So Young Patnaik, Bharat Bhusan Kang, Se Won Hwang, Hee-Ju Chung, Jong Min Song, Dae Kwon Sang, Min Kyu Patnaik, Hongray Howrelia Lee, Jae Bong Noh, Mi Young Kim, Changmu Kim, Soonok Park, Hong Seog Lee, Jun Sang Han, Yeon Soo Lee, Yong Seok |
author_sort | Park, So Young |
collection | PubMed |
description | An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species. |
format | Online Article Text |
id | pubmed-4962005 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-49620052016-08-01 Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery Park, So Young Patnaik, Bharat Bhusan Kang, Se Won Hwang, Hee-Ju Chung, Jong Min Song, Dae Kwon Sang, Min Kyu Patnaik, Hongray Howrelia Lee, Jae Bong Noh, Mi Young Kim, Changmu Kim, Soonok Park, Hong Seog Lee, Jun Sang Han, Yeon Soo Lee, Yong Seok Genes (Basel) Article An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species. MDPI 2016-07-22 /pmc/articles/PMC4962005/ /pubmed/27455329 http://dx.doi.org/10.3390/genes7070035 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Park, So Young Patnaik, Bharat Bhusan Kang, Se Won Hwang, Hee-Ju Chung, Jong Min Song, Dae Kwon Sang, Min Kyu Patnaik, Hongray Howrelia Lee, Jae Bong Noh, Mi Young Kim, Changmu Kim, Soonok Park, Hong Seog Lee, Jun Sang Han, Yeon Soo Lee, Yong Seok Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title | Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title_full | Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title_fullStr | Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title_full_unstemmed | Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title_short | Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery |
title_sort | transcriptomic analysis of the endangered neritid species clithon retropictus: de novo assembly, functional annotation, and marker discovery |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962005/ https://www.ncbi.nlm.nih.gov/pubmed/27455329 http://dx.doi.org/10.3390/genes7070035 |
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