The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis

Abstract

Cerasus humilis is endemic to China and is a new fruit tree species with economic and environmental benefits, with potential developmental and utilization applications. We report the first complete chloroplast genome sequence of C. humilis. Its genome is 158,084 bp in size, and the overall GC content is 36.8%. An inverted repeats (IR) of 52,672 bp in size is separated by a large single-copy (LSC) region of 86,374 bp and a small single-copy (SSC) region of 19,038 bp. The chloroplast genome of C. humilis contains 131 genes including 90 protein-coding genes, 33 transfer RNA genes, and 8 ribosomal RNA genes. The genome has a total 510 simple sequence repeats (SSRs). Of these, 306, 149, and 55 were found in the LSC, IR, and SSC regions, respectively. In addition, a comparison of the boundaries of the LSC, SSC, and IR regions of ten other Prunus species exhibited an overall high degree of sequence similarity, with slight variations in the IR boundary region which included gene deletions, insertions, expansions, and contractions. C. humilis lost the ycf1 gene at the IRA/SSC border and it has the largest ycf1 gene at the IRB/SSC border among these Prunus species, whereas the rps19 gene was inserted at the IRB/LSC junction. Furthermore, phylogenetic reconstruction using 61 conserved coding-protein genes clustered C. humilis with Prunus tomentosa. Thus, the complete chloroplast genome sequence of C. humilis provides a rich source of genetic information for studies on Prunus taxonomy, phylogeny, and evolution, as well as lays the foundation for further development and utilization of C. humilis.

Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

“…For the location of FP, 240, 38, and 137 microsatellite loci were detected in the LSC, SSC, and IR regions, respectively. Similar patterns were also reported in other species, such as Cerasus humilis [ 36 ], Arabis stellari [ 40 ], and Paeonia ostii [ 41 ]. However, though the total number of microsatellites was highly conserved, polymorphisms might still be observed in certain loci, which could be helpful in population and evolutionary studies [ 42 , 43 , 44 ].…”

“…The trnH gene was located in the LSC region, and was shifted 1 bp to the right, compared with the other locations. These results showed that, with the species of Acer miaotaiense , the genomic structure was highly conserved, though genomic length variation can be found in the LSC and SSC boundary regions, as reported in other species [ 36 , 38 , 39 ].…”

“…The majority of the variances occurred in the conserved non-coding regions. These results indicated the non-coding regions were less conserved, compared to coding regions, which was also found in some other species, such as Cerasus humilis [ 36 ], Talinum paniculatum [ 37 ], and Heimia myrtifolia [ 38 ].…”

The chloroplast genome of Prunus dielsiana (Rosaceae)

“…Thus, we reported a high-quality chloroplast genome (cp) of P. dielsiana to lay the foundation in the genetic recognition and functional analysis. Comparative methods of inner or outer species in the same genus also provided a new promising approach for species natural and artificial evolution in genus Cerasus (Mu et al 2018).…”

Chloroplast genome of Prunus campanulata ‘Fei han’ (Rosaceae), a new cultivar in the modern cherry breeding

“…Thus, we reported the high-quality chloroplast genome of Prunus campanulata 'Fei han' to lay the foundation in the genetic recognition and functional analysis. The comparisons of related species in same genus also provided a verification for the application of super barcode in the cherry cultivars natural and artificial evolution in genus Cerasus (Mu et al 2018).…”