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Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063475/ https://www.ncbi.nlm.nih.gov/pubmed/27736909 http://dx.doi.org/10.1371/journal.pone.0163990 |
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author | Aljohi, Hasan Awad Liu, Wanfei Lin, Qiang Zhao, Yuhui Zeng, Jingyao Alamer, Ali Alanazi, Ibrahim O. Alawad, Abdullah O. Al-Sadi, Abdullah M. Hu, Songnian Yu, Jun |
author_facet | Aljohi, Hasan Awad Liu, Wanfei Lin, Qiang Zhao, Yuhui Zeng, Jingyao Alamer, Ali Alanazi, Ibrahim O. Alawad, Abdullah O. Al-Sadi, Abdullah M. Hu, Songnian Yu, Jun |
author_sort | Aljohi, Hasan Awad |
collection | PubMed |
description | Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants. |
format | Online Article Text |
id | pubmed-5063475 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-50634752016-11-04 Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome Aljohi, Hasan Awad Liu, Wanfei Lin, Qiang Zhao, Yuhui Zeng, Jingyao Alamer, Ali Alanazi, Ibrahim O. Alawad, Abdullah O. Al-Sadi, Abdullah M. Hu, Songnian Yu, Jun PLoS One Research Article Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants. Public Library of Science 2016-10-13 /pmc/articles/PMC5063475/ /pubmed/27736909 http://dx.doi.org/10.1371/journal.pone.0163990 Text en © 2016 Aljohi et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Aljohi, Hasan Awad Liu, Wanfei Lin, Qiang Zhao, Yuhui Zeng, Jingyao Alamer, Ali Alanazi, Ibrahim O. Alawad, Abdullah O. Al-Sadi, Abdullah M. Hu, Songnian Yu, Jun Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title | Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title_full | Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title_fullStr | Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title_full_unstemmed | Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title_short | Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome |
title_sort | complete sequence and analysis of coconut palm (cocos nucifera) mitochondrial genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063475/ https://www.ncbi.nlm.nih.gov/pubmed/27736909 http://dx.doi.org/10.1371/journal.pone.0163990 |
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