Background Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated. Methods This study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China. Results The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
Background Apple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the complete chloroplast genomes of wild and cultivated apples (Malus spp.). Method We obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species. Result The chloroplast genome of Malus is highly conserved, with a genome length of 160,067–160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (psbI-atpA, psbM-psbD, and ndhC-atpE) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that Malus formed a new clade and four cultivated varieties clustered into a branch with M. sylvestris and M. sieversii, which indicated that M. sylvestris and M. sieversii were the ancestor species of the cultivated apple.
ABTRACT Handeliodendron bodinieri (Sapindaceae) is an endangered monotypic species endemic to the karst forests in southwest China whose populations are now fragmented and the total number of individuals evidently decreased. In this research, we characterized the chloroplast (cp) genome of H. bodinieri using genome skimming. The whole cp genome was 155,291 bp long and comprised 137 genes, including 8 unique rRNAs, 40 tRNAs, and 89 protein-coding genes. The overall guanine-cytosine content of H. bodinieri cp genome was 37.8%. The phylogenetic analysis suggested that H. bodinieri is closely related to the genus Mangifera . This study will be useful for future studies on conservation genetics of this economically important endemic plant.
Vernicia montana and Vernicia fordii are considered to have great economic importance in terms of having industrial oil and ornamental greening properties. However, wild resources of Vernicia trees have been reduced because of their ecology and habitat destruction. To better understand the genetic differences between V. montana and V. fordii, collecting more molecular data was necessary for further analysis. Here, we sequenced, assembled, and annotated the complete chloroplast (CP) genome of two tung trees based on the genome skimming approach. The whole CP genomes of V. montana and V. fordii were 160,906 bp and 161,494 bp in length, respectively, both of which comprised 135 genes, including 81 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 21 duplicated genes. The overall GC contents in V. montana and V. fordii CP genome were 36.13% and 36.03%, respectively. By comparing the CP genome sequences between V. montana and V. fordii, a total of 2,280 SNPs and 257 indels were identified. Among them, 1,807 SNPs and 153 indels were within the large single copy region, while 93 SNPs and 74 indels were within the small single copy region. The phylogenic analysis showed that V. montana was closely related to V. fordii and is considered a sister group. Hence, this study will be useful in investigating the conservation genetics and potential breeding applications of this oil shrub.
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