The complete chloroplast genome of the threatened Prunus cerasoides, a rare winter blooming cherry in the Himalayan region

Yang

et al. 2020

Sci Rep

Self Cite

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. The common almond (Prunus dulcis (Mill.) D.A.Webb), a member of the family Rosaceae and order Rosales, is widely and mainly distributed in the temperate zones of Europe, America, and Asia 1,2. Among the different varieties of tree nuts, almonds are the second most consumed worldwide, behind peanuts. In 2018, the volume of almonds consumed worldwide amounted to 1.19 million metric tons 1. In addition to common almonds, there are more than thirty almond species in the world, including partially cultivated and wild varieties 2. Five wild almond resources have been reported in China, including the diploid species wild almond (Prunus tenella Batsch), Mongolic almond (Prunus mongolica Maxim.), and Tangut almond (Prunus tangutica (Batalin) Koehne), the octoploid species, flowering almond (Prunus triloba Lindl.), and the dodecaploid species, longstalk almond (Prunus pedunculata (Pall.) Maxim.) 3-6. All the almond species are highly adapted to a cold and dry climate, which may indicate an important gene pool. Therefore, it is of great significance to identify the almond genetic resources and evaluate their industrial application value for effective utilization and preservation. Wild almond species usually grow in areas of altitudes between1,100 m and 2,700 m and at latitudes between 28 and 38 N and longitudes between 41 and 54 E 7,8. It is reported that there are five wild species in China, indicating that China is one of the central origins of almonds 4,5,7. Based on taxonomy, wild almond species and the common almond were classified as a separate genus, Amygdalus L....

Section: Repeat Sequence Analysismentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.)

Yang

et al. 2020

Sci Rep

Self Cite

Mitochondrial DNA Part B

“…Totally 7.9 Gb of clean data were aligned to the Prunus cerasoides complete cp genome (GenBank no. NC_035891) (Xu et al 2018) as a reference using bowtie2 v2.2.4 (Langmead and Salzberg 2012) and assembled with SPAdes v3.10.1 (Bankevich et al 2012). The final cp genome was annotated using DOGMA (Boore et al 2004), HMMER 3.1b2 (Finn et al 2011), and ARAGORN v1.2.38 (Laslett and Canback 2004).…”

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confidence: 99%

Complete chloroplast genome of Prunus canescens: an endemic shrub in China

Chen

Zong

Tong

et al. 2019

Tree Genetics & Genomes

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Yan

et al. 2021

Prunus subgenus Cerasus is a large and diverse genus. Its botanical classification has long been controversial and complicated. Molecular markers derived from the chloroplast genome may provide useful tools for phylogenetic resolution and taxonomic study in Prunus species. Thus, we compared chloroplast genomes of 23 Prunus species to identify sequences with high variation levels. The repeated sequences (RSs) and two types of sequence variation, comprising divergent homologous regions and short sequence repeats (SSRs), were identified. The species with the highest number of RSs was P. emarginata (60), whereas P. campanulata contained the highest amount of SSRs (70). In contrast, P. dictyoneura and P. yedoensis contained the lowest number of RSs (37) and SSRs (46), respectively. Out of these homologous SSRs, 11 were shared in the 23 species, and seven of them showed variations. A total of 203 homologous regions were identified. Out of these, 20 regions (19 IGSs and one intron) showed a high variation from 6.75 to 19.31%. The phylogenetic tree which was inferred based on 19 highly variable regions showed a topology similar to the one obtained using the whole chloroplast genome. We conclude that the seven variable SSRs and the 20 highly variable regions may potentially be convenient as molecular markers for phylogenetic and population genetics studies in subgenus Cerasus species. In addition, the molecular phylogenetic position of P. clarofolia was inferred based on the 19 highly variable regions.