Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)

Lu, Q and Li, H and Hong, Y and Zhang, G and Wen, S and Li, X and Zhou, G and Li, S and Liu, H and Liu, H and Liu, Z and Varshney, R K and Chen, X and Liang, X (2018) Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). Frontiers in Plant Science (TSI), 9 (604). pp. 1-15. ISSN 1664-462X

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Abstract

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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: UNSPECIFIED
Uncontrolled Keywords: Arachis ipaensis, genome sequence, genome evolution, polyploidizations, whole genome duplication, Peanut, Genomics
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 15 May 2018 04:23
Last Modified: 15 May 2018 04:23
URI: http://oar.icrisat.org/id/eprint/10659
Official URL: http://dx.doi.org/10.3389/fpls.2018.00604
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: This work was supported by the National Natural Science Foundation of China (31771841 and 31501246); the Science and Technology Planning Project of Guangdong Province (2013B050800021, 2015A030313565, 2015B020231006, 2016B020201003, 2013B020301014, 2017A030311007); the Modern Agro-industry Technology Research System (CARS-13); the Research and Demonstration of Agricultural Technology Demand in Guangdong (2016LM3161, 2016LM3164); the Key Discipline Construction of the Guangdong Academy of Agricultural Sciences (201609); and the Special Foundation of President of the Guangdong Academy of Agricultural Sciences (201831). We sincerely thank all the participants. In particular, we thank Jianan Zhang and Haofa Lan for helping us to analysis and upload the sequencing data. We thank Lesley Benyon, Ph.D., from Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.
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