Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.
Background Plums are one of the most important economic crops of the Rosaceae family and are produced all over the world. China has many local varieties, but the genomic information is limited for genetic studies. Here, we first sequenced, assembled, and analyzed the plastomes of twelve plum cultivars and developed molecular markers to distinguish them. Results The twelve plastomes of plum cultivars have a circular structure of 157,863–157,952 bp containing a large single-copy region (LSC) of 86,109–86,287 bp, a small copy region (SSC) of 18,927–19,031 bp, and two inverted repeats (IR) of 26,353–26,387 bp each. The plastomes of plum cultivars encode 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. We detected 50, 54, 54, 53, 53, 50, 54, 54, 54, 49, 50, 54 SSRs in the twelve analyzed varieties, respectively. For repeat sequences, we identified 553 tandem repeats, 204 direct repeats, and 270 palindromic repeats. We also analyzed the expansion/contraction of IR regions. The genes rpl22, rps19, rpl2, ycf1, ndhF, and the trnH span on or near the boundary of IR and single-copy regions. Phylogenetic analysis showed that the twelve cultivars were clustered with the P. salicina and P. domestica. We developed eight markers LZ01 to LZ08 based on whole plastomes and nuclear genes and validated them successfully with six repetitions. Conclusions The results obtained here could fill in the blanks of the plastomes of these twelve plum cultivars and provide a wider perspective based on the basis of the plastomes of Prunus to the molecular identification and phylogenetic construction accurately. The analysis from this study provides an important and valuable resource for studying the genetic basis for agronomic and adaptive differentiation of the Prunus species.
Prunus salicina 'Wushan plum' is a local economic fruit crop. In this study, we reported the complete chloroplast genome sequence of P. salicina 'Wushan plum'. The genome has a circular structure of 157,921 bp containing a large single-copy region (LSC) of 86,184 bp, a small copy region (SSC) of 19,031 bp, and two inverted repeats (IR) of 26,353 bp by each. It harbors 110 unique genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 28 transfer RNA genes. The phylogenomic analysis shows that P. salicina 'Wushan plum' is clustered with Prunus salicina.
Prunus tomentosa (Thunb.) Wall has high nutritional value and medicinal effects. It is widespread in China; however, most plants growing in the wild are near extinction in many places. Predicting the potential distribution of P. tomentosa under climate change is helpful for cultivating and protecting wild germplasm resources. We used two general circulation models (CCSM4 and MIROC-ESM) and two future climate scenarios (RCP4.5 and RCP8.5) to predict P. tomentosa’s present and future geographical distribution. A total of 137 distribution data points and 19 bioclimatic variables were imported into the maximum entropy model (MaxEnt). The optimal parameter combination (feature class LQHPT, regularized multiplier 3.0) was selected with corrected Akaike Information Criterion as the index. The results showed that at present and in the future, P. tomentosa was distributed across the northern provinces, with Gansu, Shanxi, Shaanxi, and Henan being the most suitable regions. Compared with the current climatic conditions, the potential growing area of P. tomentosa will move north, and the growing area will increase, especially in Xinjiang, where the low-impact zone area decreases. Temperature and humidity were the main variables affecting the potential distribution of the plant, including the average temperature in the coldest season (Bio11) and precipitation in the warmest season (Bio18).
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