Abstract
As a source of genetic variation, almond germplasm resources are of great significance in breeding. To better reveal the mutation characteristics and evolution patterns of the almond chloroplast (cp) genome, the complete cp genomes from six almond species were analyzed. The lengths of the chloroplast genome of the six almond species ranged from 157,783 bp to 158,073 bp. For repeat sequence analysis, 53 pairs of repeats (30 bp or longer) were identified. A total of 117 SSR loci were observed, including 96 polymorphic SSR loci. Nine highly variable regions with a nucleotide variability (Pi) higher than 0.08, including rps16, rps16-psbK, atpF-atpH, rpoB, ycf3-rps4, rps4-ndhJ, accD-psaI and rps7-orf42 (two highly variable regions) were located. Based on the chloroplast genome evolution analysis, three species (P. tenella, P. pedunculata and P. triloba) and wild cherry (P. tomentosa) were grouped into clade I. Clade II consisted of two species (P. mongolica and P. tangutica) and wild peach (P. davidiana). Clade III included the common almond (P. dulcis), cultivated peach (P. persica) and GanSu peach (P. kansuensis). This result expands the researchers’ vision of almond plant diversity and promotes an understanding of the evolutionary relationship among almond species. In brief, this study provides abundant resources for the study of the almond chloroplast genome, and has an important reference value for study of the evolution and species identification of almond.
Highlights
Wild almond species usually grow in areas of altitudes between[1,100] m and 2,700 m and at latitudes between 28 and 38 N and longitudes between 41 and 54 E7,8
Among the six almonds species sequenced in this research, 2874 Mb to 4311 Mb of raw data was generated on the Illumina sequencing system, with an average read length of 150 bp
We report the chloroplast genomes of five almond species by de novo sequencing and compare them with one previously published almond cp genome sequence
Summary
Wild almond species usually grow in areas of altitudes between[1,100] m and 2,700 m and at latitudes between 28 and 38 N and longitudes between 41 and 54 E7,8. Our research purposes were as follows: (1) to study the overall structure of the cp genomes; (2) to detect the variations in the repeat sequences and the simple sequence repeats (SSRs) in the six almond cp genomes; (3) to screen rapidly evolving DNA regions in the six chloroplast genomes; and (4) to analyze the phylogenetic relationship using the sequence data of the chloroplast genome. These results will supply rich molecular tools for further phylogenetic analysis, population genetics analysis, and species identification and will contribute to almond breeding
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