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Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)

Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome o...

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Autores principales: Govindharaj, Guru-Pirasanna-Pandi, Babu, Soumya Bharti, Choudhary, Jaipal Singh, Asad, Muhammad, Chidambaranathan, Parameswaran, Gadratagi, Basana-Gowda, Rath, Prakash Chandra, Naaz, Naiyar, Jaremko, Mariusz, Qureshi, Kamal Ahmad, Kumar, Uttam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506247/
https://www.ncbi.nlm.nih.gov/pubmed/36143326
http://dx.doi.org/10.3390/life12091289
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author Govindharaj, Guru-Pirasanna-Pandi
Babu, Soumya Bharti
Choudhary, Jaipal Singh
Asad, Muhammad
Chidambaranathan, Parameswaran
Gadratagi, Basana-Gowda
Rath, Prakash Chandra
Naaz, Naiyar
Jaremko, Mariusz
Qureshi, Kamal Ahmad
Kumar, Uttam
author_facet Govindharaj, Guru-Pirasanna-Pandi
Babu, Soumya Bharti
Choudhary, Jaipal Singh
Asad, Muhammad
Chidambaranathan, Parameswaran
Gadratagi, Basana-Gowda
Rath, Prakash Chandra
Naaz, Naiyar
Jaremko, Mariusz
Qureshi, Kamal Ahmad
Kumar, Uttam
author_sort Govindharaj, Guru-Pirasanna-Pandi
collection PubMed
description Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.
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spelling pubmed-95062472022-09-24 Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS) Govindharaj, Guru-Pirasanna-Pandi Babu, Soumya Bharti Choudhary, Jaipal Singh Asad, Muhammad Chidambaranathan, Parameswaran Gadratagi, Basana-Gowda Rath, Prakash Chandra Naaz, Naiyar Jaremko, Mariusz Qureshi, Kamal Ahmad Kumar, Uttam Life (Basel) Article Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens. MDPI 2022-08-23 /pmc/articles/PMC9506247/ /pubmed/36143326 http://dx.doi.org/10.3390/life12091289 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Govindharaj, Guru-Pirasanna-Pandi
Babu, Soumya Bharti
Choudhary, Jaipal Singh
Asad, Muhammad
Chidambaranathan, Parameswaran
Gadratagi, Basana-Gowda
Rath, Prakash Chandra
Naaz, Naiyar
Jaremko, Mariusz
Qureshi, Kamal Ahmad
Kumar, Uttam
Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title_full Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title_fullStr Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title_full_unstemmed Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title_short Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)
title_sort genome organization and comparative evolutionary mitochondriomics of brown planthopper, nilaparvata lugens biotype 4 using next generation sequencing (ngs)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506247/
https://www.ncbi.nlm.nih.gov/pubmed/36143326
http://dx.doi.org/10.3390/life12091289
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