ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica
Tóm tắt
Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.
Tài liệu tham khảo
Arus P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012) The peach genome. Tree Genet Gen 8:531–547
Cao K, Zheng Z, Wang L, Liu X, Zhu G, Fang W, Cheng S, Zeng P, Chen C, Wang X, Xie M (2014) Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol 15:415
Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494
Jansen RK, Saski CA, Lee S, Hansen AK, Daniell H (2010) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28:835–847
Khan A, Asaf S, Khan AL, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Khan A, Shehzad T, Alsaady N, Al-Lawati A, Al-Rawahi A (2019) First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees. PLoS One 14(1):e0208511
Douglas SE (1990) Plastid evolution: origins, diversity, trends. Curr Opin Genet Dev 8:655–661
Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134
Yu Y, Fu J, Xu Y, Zhang J, Ren F, Zhao H, Tian S, Guo W, Tu X, Zhao J, Jiang D (2018) Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Nat Commun 9:5404
Jeon, J.H., and Kim, S.C., (2019). Comparative Analysis of the complete chloroplast genome sequences of three closely related East-Asian wild roses (Rosa sect. Synstylae; Rosaceae). Genes 10:23
Li Y, Zhang J, Li L, Gao L, Xu J, Yang M (2018) Structural and comparative analysis of the complete chloroplast genome of pyrus hopeiensis—“wild plants with a tiny population”—and three other pyrus species. Int J Mol Sci 19(10):p.3262
Pervaiz T, Sun X, Zhang Y, Tao R, Zhang J, Fang J (2015) Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biol 15:1–10
Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, Cheng T, Guo J, Zhou S (2015) ycf1, the most promising plastid DNA barcode of land plants. Sci Rep 5:p.8348
Thomson AM, Vargas OM, Dick CW (2017) Comparative analysis of 24 chloroplast genomes yields highly informative genetic markers for the Brazil nut family (Lecythidaceae). bioRxiv:192112
Krawczyk K, Nobis M, Myszczyński K, Klichowska E, Sawicki J (2018) Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa). Sci Rep 8:1924
Wang S, Shi C, Gao LZ (2013) Plastid genome sequence of a wild woody oil species, Prinsepia utilis, provides insights into evolutionary and mutational patterns of Rosaceae chloroplast genomes. PLoS One 8:e73946
Choi KS, Chung MG, Park S (2016) The complete chloroplast genome sequences of three veroniceae species (Plantaginaceae): comparative analysis and highly divergent regions. Front Plant Sci 7:355
Bi Y, Zhang MF, Xue J, Dong R, Du YP, Zhang XH (2018) Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep 8:1184
Dong W, Liu J, Yu J, Wang L, Zhou S (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PloS One 7:e35071
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549
Metsalu T, Vilo J (2015) ClustVis: A web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res 43:W566–W570
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA et al (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266:5–43
Song Y, Dong W, Liu B, Xu C, Yao X, Gao J, Corlett RT (2015) Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front Plant Sci 6:662–662
Rohwer JG, Li J, Rudolph B, Schmidt SA, VWH LHW (2009) Is Persea (Lauraceae) monophyletic. Evidence from nuclear ribosomal ITS sequences. Taxon 58:1153–1167
Amar MH, Hassan AH, Biswas MK, Dulloo E, Xie ZZ, Guo WW (2014) Maximum parsimony based resolution of inter-species phylogenetic relationships in Citrus L. (Rutaceae) using ITS of rDNA. Biotechnol Biotechnol Equip 28:61–67
Guo C, Mcdowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, Reddy TE (2017) Transversions have larger regulatory effects than transitions. BMC Genomics 18:394
Korotkova N, Nauheimer L, Ter-Voskanyan H, Allgaier M, Borsch T (2014) Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae) and other angiosperms for marker choice. PLoS One 9(11):e112998
Meng D, Xiaomei Z, Wenzhen K, Xu Z (2019) Detecting useful genetic markers and reconstructing the phylogeny of an important medicinal resource plant, Artemisia selengensis , based on chloroplast genomics. PLoS One 14(2):e0211340
Wang J, Li C, Yan C, Zhao X, Shan S (2018) A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties. PeerJ 6:e5349
Cao Y, Luo Q, Tian Y, Meng F (2017) Physiological and proteomic analyses of the drought stress response in Amygdalus mira (Koehne) Yü et Lu roots. BMC plant biology 17:53
Biswajit D, Ahmed N, Pushkar S (2011) Prunus diversity-early and present development. a review. Int J Bio Diverse Conserv 3:721–734
Yazbek M, Oh SH (2013) Peaches and almonds: phylogeny of Prunus subg. Amygdalus (Rosaceae) based on DNA sequences and morphology. Plant Syst Evol 299:1403–1418
Feng Y, Liu T, Wang XY, Li BB, Liang CL, Cai YL (2018) Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae). Conserv Genet Resour 10:85–88