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Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars
Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One o...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981771/ https://www.ncbi.nlm.nih.gov/pubmed/24718264 http://dx.doi.org/10.1371/journal.pone.0094158 |
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author | Sabir, Jamal S. M. Arasappan, Dhivya Bahieldin, Ahmed Abo-Aba, Salah Bafeel, Sameera Zari, Talal A. Edris, Sherif Shokry, Ahmed M. Gadalla, Nour O. Ramadan, Ahmed M. Atef, Ahmed Al-Kordy, Magdy A. El-Domyati, Fotoh M. Jansen, Robert K. |
author_facet | Sabir, Jamal S. M. Arasappan, Dhivya Bahieldin, Ahmed Abo-Aba, Salah Bafeel, Sameera Zari, Talal A. Edris, Sherif Shokry, Ahmed M. Gadalla, Nour O. Ramadan, Ahmed M. Atef, Ahmed Al-Kordy, Magdy A. El-Domyati, Fotoh M. Jansen, Robert K. |
author_sort | Sabir, Jamal S. M. |
collection | PubMed |
description | Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One of the major limitations of these efforts is the uncertainty regarding the number of date palm cultivars, which are currently based on fruit shape, size, color, and taste. Whole mitochondrial and plastid genome sequences were utilized to examine single nucleotide polymorphisms (SNPs) of date palms to evaluate the efficacy of this approach for molecular characterization of cultivars. Mitochondrial and plastid genomes of nine Saudi Arabian cultivars were sequenced. For each species about 60 million 100 bp paired-end reads were generated from total genomic DNA using the Illumina HiSeq 2000 platform. For each cultivar, sequences were aligned separately to the published date palm plastid and mitochondrial reference genomes, and SNPs were identified. The results identified cultivar-specific SNPs for eight of the nine cultivars. Two previous SNP analyses of mitochondrial and plastid genomes identified substantial intra-cultivar ( = intra-varietal) polymorphisms in organellar genomes but these studies did not properly take into account the fact that nearly half of the plastid genome has been integrated into the mitochondrial genome. Filtering all sequencing reads that mapped to both organellar genomes nearly eliminated mitochondrial heteroplasmy but all plastid SNPs remained heteroplasmic. This investigation provides valuable insights into how to deal with interorganellar DNA transfer in performing SNP analyses from total genomic DNA. The results confirm recent suggestions that plastid heteroplasmy is much more common than previously thought. Finally, low levels of sequence variation in plastid and mitochondrial genomes argue for using nuclear SNPs for molecular characterization of date palm cultivars. |
format | Online Article Text |
id | pubmed-3981771 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39817712014-04-11 Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars Sabir, Jamal S. M. Arasappan, Dhivya Bahieldin, Ahmed Abo-Aba, Salah Bafeel, Sameera Zari, Talal A. Edris, Sherif Shokry, Ahmed M. Gadalla, Nour O. Ramadan, Ahmed M. Atef, Ahmed Al-Kordy, Magdy A. El-Domyati, Fotoh M. Jansen, Robert K. PLoS One Research Article Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One of the major limitations of these efforts is the uncertainty regarding the number of date palm cultivars, which are currently based on fruit shape, size, color, and taste. Whole mitochondrial and plastid genome sequences were utilized to examine single nucleotide polymorphisms (SNPs) of date palms to evaluate the efficacy of this approach for molecular characterization of cultivars. Mitochondrial and plastid genomes of nine Saudi Arabian cultivars were sequenced. For each species about 60 million 100 bp paired-end reads were generated from total genomic DNA using the Illumina HiSeq 2000 platform. For each cultivar, sequences were aligned separately to the published date palm plastid and mitochondrial reference genomes, and SNPs were identified. The results identified cultivar-specific SNPs for eight of the nine cultivars. Two previous SNP analyses of mitochondrial and plastid genomes identified substantial intra-cultivar ( = intra-varietal) polymorphisms in organellar genomes but these studies did not properly take into account the fact that nearly half of the plastid genome has been integrated into the mitochondrial genome. Filtering all sequencing reads that mapped to both organellar genomes nearly eliminated mitochondrial heteroplasmy but all plastid SNPs remained heteroplasmic. This investigation provides valuable insights into how to deal with interorganellar DNA transfer in performing SNP analyses from total genomic DNA. The results confirm recent suggestions that plastid heteroplasmy is much more common than previously thought. Finally, low levels of sequence variation in plastid and mitochondrial genomes argue for using nuclear SNPs for molecular characterization of date palm cultivars. Public Library of Science 2014-04-09 /pmc/articles/PMC3981771/ /pubmed/24718264 http://dx.doi.org/10.1371/journal.pone.0094158 Text en © 2014 Sabir 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Sabir, Jamal S. M. Arasappan, Dhivya Bahieldin, Ahmed Abo-Aba, Salah Bafeel, Sameera Zari, Talal A. Edris, Sherif Shokry, Ahmed M. Gadalla, Nour O. Ramadan, Ahmed M. Atef, Ahmed Al-Kordy, Magdy A. El-Domyati, Fotoh M. Jansen, Robert K. Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title | Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title_full | Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title_fullStr | Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title_full_unstemmed | Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title_short | Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars |
title_sort | whole mitochondrial and plastid genome snp analysis of nine date palm cultivars reveals plastid heteroplasmy and close phylogenetic relationships among cultivars |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981771/ https://www.ncbi.nlm.nih.gov/pubmed/24718264 http://dx.doi.org/10.1371/journal.pone.0094158 |
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