Phylogeography of Prunus Armeniaca L. Revealed by Chloroplast DNA and Nuclear Ribosomal Sequences

Overview

Journal Sci Rep

Specialty Science

Date 2021 Jul 2

PMID 34211010

Citations 4

Authors

Wen-Wen Li

Li-Qiang Liu

Qiu-Ping Zhang

Wei-Quan Zhou

Guo-Quan Fan

Kang Liao

Affiliations

Soon will be listed here.

Abstract

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: H = 0.499; ITS: H = 0.876) and a low level of genetic differentiation (cpDNA: F = 0.1628; ITS: F = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (N) was significantly higher than the number of substitution types (G), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Citing Articles

Across a phylogeographic break in the Qinling Mountains-Huaihe River Line: Quaternary evolutionary history of a medicinal and edible homologous plant (Allium macrostemon) in China.

Jiang C, Shi T, Mo Z, Zhao C BMC Ecol Evol. 2024; 24(1):107.

PMID: 39138401 PMC: 11323607. DOI: 10.1186/s12862-024-02297-0.

Assessing the phylogenetic relationship among varieties of (Meliaceae) in sympatry with chloroplast genomes.

Xiao Y, Wang X, He Z, Lv Y, Zhang C, Hu X Ecol Evol. 2023; 13(12):e10828.

PMID: 38094154 PMC: 10716671. DOI: 10.1002/ece3.10828.

Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach.

Jamdade R, Al-Shaer K, Al-Sallani M, Al-Harthi E, Mahmoud T, Gairola S PLoS One. 2022; 17(7):e0270463.

PMID: 35895732 PMC: 9328517. DOI: 10.1371/journal.pone.0270463.

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae).

Li D, Li J, Wang D, Xu Y, Zhu G BMC Plant Biol. 2021; 21(1):558.

PMID: 34814832 PMC: 8611967. DOI: 10.1186/s12870-021-03315-9.

References

Zhang Q, Chen X, Guo H, Trindade L, Salentijn E, Guo R . Latitudinal Adaptation and Genetic Insights Into the Origins of L. Front Plant Sci. 2019; 9:1876. PMC: 6309158. DOI: 10.3389/fpls.2018.01876. View

Meng H, Zhang M . Diversification of plant species in arid Northwest China: species-level phylogeographical history of Lagochilus Bunge ex Bentham (Lamiaceae). Mol Phylogenet Evol. 2013; 68(3):398-409. DOI: 10.1016/j.ympev.2013.04.012. View

Jaramillo-Correa J, Beaulieu J, Bousquet J . Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Mol Ecol. 2004; 13(9):2735-47. DOI: 10.1111/j.1365-294X.2004.02258.x. View

Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard J . The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events. Mol Ecol. 2019; 28(24):5299-5314. DOI: 10.1111/mec.15296. View

Yang J, Vazquez L, Feng L, Liu Z, Zhao G . Climatic and Soil Factors Shape the Demographical History and Genetic Diversity of a Deciduous Oak () in Northern China. Front Plant Sci. 2018; 9:1534. PMC: 6209687. DOI: 10.3389/fpls.2018.01534. View

Anderson L, Hu F, Nelson D, Petit R, Paige K . Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proc Natl Acad Sci U S A. 2006; 103(33):12447-50. PMC: 1567899. DOI: 10.1073/pnas.0605310103. View

Dutech C, Maggia L, I Joly H . Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree. Mol Ecol. 2000; 9(9):1427-32. DOI: 10.1046/j.1365-294x.2000.01027.x. View

Zhang X, Shen S, Wu F, Wang Y . Inferring Genetic Variation and Demographic History of Franch. (Magnoliaceae) from Chloroplast DNA Sequences and Microsatellite Markers. Front Plant Sci. 2017; 8:583. PMC: 5399939. DOI: 10.3389/fpls.2017.00583. View

Excoffier L, Lischer H . Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2011; 10(3):564-7. DOI: 10.1111/j.1755-0998.2010.02847.x. View

10.

Afzal-Rafii Z, Dodd R . Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe. Mol Ecol. 2007; 16(4):723-36. DOI: 10.1111/j.1365-294X.2006.03183.x. View

11.

Wolfe K, Li W, Sharp P . Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 1987; 84(24):9054-8. PMC: 299690. DOI: 10.1073/pnas.84.24.9054. View

12.

Pennington R, Lavin M, Sarkinen T, Lewis G, Klitgaard B, Hughes C . Contrasting plant diversification histories within the Andean biodiversity hotspot. Proc Natl Acad Sci U S A. 2010; 107(31):13783-7. PMC: 2922214. DOI: 10.1073/pnas.1001317107. View

13.

Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S . ycf1, the most promising plastid DNA barcode of land plants. Sci Rep. 2015; 5:8348. PMC: 4325322. DOI: 10.1038/srep08348. View

14.

Salvi D, Schembri P, Sciberras A, Harris D . Evolutionary history of the Maltese wall lizard Podarcis filfolensis: insights on the ‘Expansion–Contraction’ model of Pleistocene biogeography. Mol Ecol. 2014; 23(5):1167-87. DOI: 10.1111/mec.12668. View

15.

Simmons M, Ochoterena H . Gaps as characters in sequence-based phylogenetic analyses. Syst Biol. 2002; 49(2):369-81. View

16.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

17.

Zhebentyayeva T, Reighard G, Gorina V, Abbott A . Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm. Theor Appl Genet. 2003; 106(3):435-44. DOI: 10.1007/s00122-002-1069-z. View

18.

Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard J . New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Mol Ecol. 2016; 25(19):4712-29. DOI: 10.1111/mec.13772. View

19.

Li Y, Gao Q, Gengji Z, Jia L, Wang Z, Chen S . Rapid Intraspecific Diversification of the Alpine Species (Saxifragaceae) in the Qinghai-Tibetan Plateau and Himalayas. Front Genet. 2018; 9:381. PMC: 6153349. DOI: 10.3389/fgene.2018.00381. View

20.

Willis K, Niklas K . The role of Quaternary environmental change in plant macroevolution: the exception or the rule?. Philos Trans R Soc Lond B Biol Sci. 2004; 359(1442):159-72. PMC: 1693324. DOI: 10.1098/rstb.2003.1387. View