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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...

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Autores principales: 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
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
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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.
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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
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