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Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers
Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736913/ https://www.ncbi.nlm.nih.gov/pubmed/26881195 http://dx.doi.org/10.1155/2016/4169587 |
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author | Patnaik, Bharat Bhusan Park, So Young Kang, Se Won Hwang, Hee-Ju 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 Park, So Young Kang, Se Won Hwang, Hee-Ju 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 | Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp. |
format | Online Article Text |
id | pubmed-4736913 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-47369132016-02-15 Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers Patnaik, Bharat Bhusan Park, So Young Kang, Se Won Hwang, Hee-Ju 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 Genomics Research Article Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp. Hindawi Publishing Corporation 2016 2016-01-10 /pmc/articles/PMC4736913/ /pubmed/26881195 http://dx.doi.org/10.1155/2016/4169587 Text en Copyright © 2016 Bharat Bhusan Patnaik et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Patnaik, Bharat Bhusan Park, So Young Kang, Se Won Hwang, Hee-Ju 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 Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title | Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title_full | Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title_fullStr | Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title_full_unstemmed | Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title_short | Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers |
title_sort | transcriptome profile of the asian giant hornet (vespa mandarinia) using illumina hiseq 4000 sequencing: de novo assembly, functional annotation, and discovery of ssr markers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736913/ https://www.ncbi.nlm.nih.gov/pubmed/26881195 http://dx.doi.org/10.1155/2016/4169587 |
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