Cargando…
Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)
Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respective...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943715/ https://www.ncbi.nlm.nih.gov/pubmed/29774047 http://dx.doi.org/10.3389/fpls.2018.00604 |
_version_ | 1783321681260969984 |
---|---|
author | Lu, Qing Li, Haifen Hong, Yanbin Zhang, Guoqiang Wen, Shijie Li, Xingyu Zhou, Guiyuan Li, Shaoxiong Liu, Hao Liu, Haiyan Liu, Zhongjian Varshney, Rajeev K. Chen, Xiaoping Liang, Xuanqiang |
author_facet | Lu, Qing Li, Haifen Hong, Yanbin Zhang, Guoqiang Wen, Shijie Li, Xingyu Zhou, Guiyuan Li, Shaoxiong Liu, Hao Liu, Haiyan Liu, Zhongjian Varshney, Rajeev K. Chen, Xiaoping Liang, Xuanqiang |
author_sort | Lu, Qing |
collection | PubMed |
description | Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A. ipaensis and A. duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A. hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome. |
format | Online Article Text |
id | pubmed-5943715 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-59437152018-05-17 Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) Lu, Qing Li, Haifen Hong, Yanbin Zhang, Guoqiang Wen, Shijie Li, Xingyu Zhou, Guiyuan Li, Shaoxiong Liu, Hao Liu, Haiyan Liu, Zhongjian Varshney, Rajeev K. Chen, Xiaoping Liang, Xuanqiang Front Plant Sci Plant Science Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A. ipaensis and A. duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A. hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome. Frontiers Media S.A. 2018-05-03 /pmc/articles/PMC5943715/ /pubmed/29774047 http://dx.doi.org/10.3389/fpls.2018.00604 Text en Copyright © 2018 Lu, Li, Hong, Zhang, Wen, Li, Zhou, Li, Liu, Liu, Liu, Varshney, Chen and Liang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Lu, Qing Li, Haifen Hong, Yanbin Zhang, Guoqiang Wen, Shijie Li, Xingyu Zhou, Guiyuan Li, Shaoxiong Liu, Hao Liu, Haiyan Liu, Zhongjian Varshney, Rajeev K. Chen, Xiaoping Liang, Xuanqiang Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title | Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title_full | Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title_fullStr | Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title_full_unstemmed | Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title_short | Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis) |
title_sort | genome sequencing and analysis of the peanut b-genome progenitor (arachis ipaensis) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943715/ https://www.ncbi.nlm.nih.gov/pubmed/29774047 http://dx.doi.org/10.3389/fpls.2018.00604 |
work_keys_str_mv | AT luqing genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT lihaifen genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT hongyanbin genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT zhangguoqiang genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT wenshijie genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT lixingyu genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT zhouguiyuan genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT lishaoxiong genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT liuhao genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT liuhaiyan genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT liuzhongjian genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT varshneyrajeevk genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT chenxiaoping genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis AT liangxuanqiang genomesequencingandanalysisofthepeanutbgenomeprogenitorarachisipaensis |