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Twelve complete chloroplast genomes of wild peanuts : great genetic resources and a better understanding of Arachis phylogeny

Wang, Juan ; Li, Yuan LU ; Li, Chunjuan ; Yan, Caixia ; Zhao, Xiaobo ; Yuan, Cuiling ; Sun, Quanxi ; Shi, Chengren and Shan, Shihua (2019) In BMC Plant Biology 19(1).
Abstract

BACKGROUND: The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. RESULTS: Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These... (More)

BACKGROUND: The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. RESULTS: Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. CONCLUSION: In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.

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author
; ; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Arachis, Chloroplast genome, Genetic variation, Genome type, Peanut, Phylogeny, SNDs, SSRs
in
BMC Plant Biology
volume
19
issue
1
article number
504
publisher
BioMed Central (BMC)
external identifiers
  • scopus:85075295034
  • pmid:31744457
ISSN
1471-2229
DOI
10.1186/s12870-019-2121-3
language
English
LU publication?
yes
id
f98d05f7-4940-425d-a282-465ed5e674b4
date added to LUP
2019-12-05 09:02:55
date last changed
2024-04-02 20:35:42
@article{f98d05f7-4940-425d-a282-465ed5e674b4,
  abstract     = {{<p>BACKGROUND: The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. RESULTS: Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I &amp; II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. CONCLUSION: In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.</p>}},
  author       = {{Wang, Juan and Li, Yuan and Li, Chunjuan and Yan, Caixia and Zhao, Xiaobo and Yuan, Cuiling and Sun, Quanxi and Shi, Chengren and Shan, Shihua}},
  issn         = {{1471-2229}},
  keywords     = {{Arachis; Chloroplast genome; Genetic variation; Genome type; Peanut; Phylogeny; SNDs; SSRs}},
  language     = {{eng}},
  month        = {{11}},
  number       = {{1}},
  publisher    = {{BioMed Central (BMC)}},
  series       = {{BMC Plant Biology}},
  title        = {{Twelve complete chloroplast genomes of wild peanuts : great genetic resources and a better understanding of Arachis phylogeny}},
  url          = {{http://dx.doi.org/10.1186/s12870-019-2121-3}},
  doi          = {{10.1186/s12870-019-2121-3}},
  volume       = {{19}},
  year         = {{2019}},
}