Author:
Zhou Jiawei,He Wenchuang,Wang Jie,Liao Xuezhu,Xiang Kunli,Ma Mingchuan,Liu Zhang,Li Yongyao,Tembrock Luke R.,Wu Zhiqiang,Liu Longlong
Abstract
Abstract
Background
Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated.
Results
In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya.
Conclusions
The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.
Funder
the Agricultural Science and Technology Innovation Project of Shanxi Agricultural University
the China Agriculture Research System of MOF and MARA
the National Natural Science Foundation of China
the Science, Technology, and Innovation Commission of Shenzhen Municipality
the Elite Young Scientists Program of the Chinese Academy of Agricultural Sciences
Science Technology and Innovation Commission of Shenzhen Municipality of China
Publisher
Springer Science and Business Media LLC
Reference62 articles.
1. Fan Y, Jin YN, Ding MQ, Tang Y, Cheng JP, Zhang KX, et al. The complete chloroplast genome sequences of eight Fagopyrum species: insights into genome evolution and phylogenetic relationships. Front Plant Sci. 2021;12:799904.
2. Zhang KX, He M, Fan Y, Zhao H, Gao B, Yang KL, et al. Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits. Genome Biol. 2021;22(1):23.
3. Joshi DC, Zhang KX, Wang CL, Chandora R, Khurshid M, Li JB, et al. Strategic enhancement of genetic gain for nutraceutical development in buckwheat: a genomics-driven perspective. Biotechnol Adv. 2020;39:107479.
4. Joshi DC, Chaudhari GV, Sood S, Kant L, Pattanayak A, Zhang KX, et al. Revisiting the versatile buckwheat: reinvigorating genetic gains through integrated breeding and genomics approach. Planta. 2019;250(3):783–801.
5. Hunt HV, Shang X, Jones MK. Buckwheat: a crop from outside the major Chinese domestication centres? A review of the archaeobotanical, palynological and genetic evidence. Veg Hist Archaeobot. 2018;27(3):493–506.
Cited by
3 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献