Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

Abstract

Malus hupehensis belongs to the Malus genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of Malus hupehensis, using a Hiseq X Ten sequencing platform, is reported. The M. hupehensis cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine Malus complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that M. hupehensis clustered closer ties with M. baccata, M. micromalus, and M. prunifolia than with M. tschonoskii. The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the Malus and related species.

Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula

“…Therefore, it is yet to be ascertained whether the conserved SSR motifs found in the four Rubus species of subgenus Anoplobatus and Idaeobatus in this study can also be found in other major lineages of Rubus , such as subgenus Malachobatus and Rubus . The locations of SSR motifs and A/T abundance found in R. boninensis , R. trifidus , and R. crataegifolius (Figure 2B) were consistent with other members of Rosaceae [39,44,45,46,47]. As the utility of cpSSRs has been proven to be valuable in various plant lineages (e.g., Glycine , [48]; Pinus , [49]; Triticum , [50]; Abies , [51]; Cucumis , [52]), we believe that the cpSSR markers developed in this study can be useful for complex studies at both the population and specific level of members of subgenus Anoplobatus and Idaeobatus .…”

“…spontanea (11.8%; n = 10). Also, the highest proportions of mononucleotides motifs were found in nine species of Malus chloroplast genomes, with the total number of chloroplast SSR (cpSSRs) ranging from 94 to 101 [46]. Therefore, it is yet to be ascertained whether the conserved SSR motifs found in the four Rubus species of subgenus Anoplobatus and Idaeobatus in this study can also be found in other major lineages of Rubus , such as subgenus Malachobatus and Rubus .…”

“…Based on three Pyrus chloroplast genome sequences, four hotspot regions (i.e., petN-psbM, psbM-trnD, rps4-trnT-trnL , and psaI-ycf4 ) with an average Pi value as 0.00054 were suggested as effective makers for phylogeny and conservation genetics in the genus Pyrus [56]. In nine Malus chloroplast genomes, some divergence in intergenic spacer and introns was found, including trnK/rps16, trnT/trnL , and clpP introns and coding regions (matK, rpoA, ndhF , and ycf1 ) [46]. In Rosa section Synstylae , closely related taxa in the same subfamily Rosoideae as Rubus , Jeon and Kim [39] found six highly variable regions with Pi value of >0.006: psbI-trnS-trnG , 5’ matK-trnK , rps16-trnG, rpoB-trnC, rps4-trnT , and ycf1 .…”

Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

“…A highly variable region or hotspot region in the whole chloroplast genome scale can help elucidate the phylogenetic relationships and complex evolutionary history of Rubus as a maternally inherited marker. Recently, several hot spot regions including genic and non-coding regions across the entire plastome were reported in several members of Rosaceae, such as Malus 56 , Prunus 57 , Pyrus 27 , and Rosa 30 . In our current study, we also detected four highly variable regions, including rps16 / trnQ ( Pi = 0.0518) and petA / psbJ ( Pi = 0.0466), as two of the most variable hotspots within the eight Taiwan Rubus endemics, with an average nucleotide diversity ( Pi ) value of 0.01.…”

Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

“…All nine species of the genus Artemisia showed similarity in terms of the gene content, intron content, and composition of GC content. The chloroplast genome of angiosperms is highly conserved and several previous studies have also reported high similarity in chloroplast genome sequences of the same lineage [26,31,32,33,34,35]. However, some studies have reported variation in gene numbers and gain or loss of introns at a genus level, as well as at a family level [36,37,38].…”