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Ranunculaceae is a large family of angiosperms comprising 2500 known species—a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I . anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum . The circular mitogenome of I . anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I . anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I . anemonoides , including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes ( nad1 and rpl5 ) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites ( atp6 and mttB ) were detected in the I . anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I . anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I . anemonoides . Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I . anemonoides .

Background Vernicia montana and V . fordii are economically important woody oil species in the Euphorbiaceae that have great industrial oil and ornamental greening properties, however, the wild resources of Vernicia trees have been reduced because of their habitat destruction. Considering the diverse economic and ecological importance of Vernicia species, it is important to collect more molecular data to determine the genetic differences between V. montana and V. fordii . Results 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 163,518 bp and 161,495 bp in length, both including a pair of inverted repeats separated by a large single-copy and a small single-copy region. We detected a total number of 311 tandem repeats, 100 dispersed repeats, and 255 simple repeats from V. montana and V. fordii CP genomes. The mean value of nucleotide diversity between the two species was 0.0122, and the average Ka/Ks ratio across all coding genes was 0.3483. Comparative chloroplast genome analysis showed that the coding regions were more conserved than the non-coding regions. The phylogenetic relationships yielded by the complete genome sequences showed that V. montana was closely related to V. fordii and is considered as a sister group. Conclusions We sequenced, assembled, annotated, and analyzed the CP genome of two tung trees, which will be useful in investigating the conservation genetics and potential breeding applications of this oil shrub.

Background Limonium Mill., a genus belonging to the family Plumbaginaceae, is mainly distributed along the Mediterranean coast of Eurasia. It is known for its rich species diversity and remarkable morphological variation, encompassing both herbaceous and semi-shrub forms. Some species of Limonium have medicinal, economic, and ornamental value in China. However, their genomic and phylogenetic relationships remain unclear. In this study, we sequenced and assembled complete chloroplast genomes of eight Limonium species to address this issue. We conducted comparative and phylogenetic analyses to investigate the genetic structural characteristics and clarify the taxonomic status of 12 Limonium species. Results The newly obtained circular chloroplast genomes of the eight Limonium species had a quadripartite structure and ranged from 154,545 to 154,960 bp in length. All species contained 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Despite minor variations in the inverted repeat (IR) boundary regions, the overall genome structure and gene content remained relatively conserved. The rpl16 gene lost its intron and the rpl23 gene underwent pseudogenization. We identified 55–73 SSRs repeat sequences and three nucleotide diversity regions that will be used for population genetics and molecular phylogenetic studies of the Limonium genus. The robust phylogenetic tree suggests that species belonging to these sections in Xinjiang, China, have accumulated substantial genetic divergence over long-term evolution, resulting in stable phylogenetic relationships. Conclusion The complete chloroplast genomes of Limonium increase our understanding of the genetic diversity and evolution of Limonium species and further aid in the exploration and utilization of Limonium plants.

Background Pitaya is an important tropical fruit highly favoured by consumers owing to its good and juicy characteristics. It contains a large amount of betacyanin, which is a natural food-colouring agent, in the peel and pulp. However, few studies have focused on the pitaya chloroplast (cp) genomes. Results To explore the genetic differences and phylogenetic relationships among the cp genomes of the six pitaya cultivars, we assembled, annotated, and performed a comparative genomic analysis. The cp genomes of the six cultivars exhibited a typical circular structure, ranging in length from 133,146 to 133,617 bp, with a GC content of 36.4%. All individual cp genomes were annotated with 123 genes, including 80 protein-coding genes, 38 tRNA genes, four rRNA genes, and one pseudogene ( ycf 68). Six mutated hotspot regions ( trn F-GAA- rbc L, trn M-CAU- acc D, rpl 20- psb B, acc D, rpl 22, ycf 1) were detected, which could be considered potential molecular markers for population genetics and molecular phylogeny studies. Phylogenetic analysis showed that pitaya cultivars clustered into a single branch in the phylogenetic tree of the Cactaceae family. Furthermore, the observed phylogenetic patterns suggest a complex genetic basis for colour variation among pitaya cultivars. Conclusions The study findings expand our understanding of the cp genome of pitaya and the phylogenetic relationships among different cultivars. The genomic data obtained provide important information for the breeding and genetic improvement of pitaya.

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. 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. 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.

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 ( spp.). 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. The chloroplast genome of 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 ( I- A, M- D, and C- E) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that formed a new clade and four cultivated varieties clustered into a branch with and , which indicated that and were the ancestor species of the cultivated apple.

is an endangered species endemic to the tropical Hainan Island in southern China and of historical importance for Chinese medicine. It is currently the only unplaced species of the genus (Euphorbiaceae) due to its isolated island distribution and debated placement by a previous molecular phylogenetic study. We sequenced nuclear ITS and chloroplast and for newly collected accessions of and additional species found in Hainan, and analyzed the sequences in the context of the entire genus together with published data. All gene regions highly supported that occupied an isolated phylogenetic position, showing no close affinity with any known sections suggesting it was a new section. ITS placed sister to sect. (subgenus ) from Brazil with an estimated divergence time of 9.3-30.6 Mya while the chloroplast markers placed at a position sister to the entire New World clade of subgenus . In addition, our karyological results suggested a close affinity between and the New World species of subg. , with which shared the same chromosome number 2n = 28 and basic chromosome number x = 7. Phenotypically, is unique with no close resemblance to other species in subg. . Based on its isolated biogeographical, karyological, and phenotypical position, we propose a new section . subgenus section that might origin from long distance dispersal events because collective evidences showed a close affinity between the species from the Old World with those from the New World.

The mango is an important economic crop with a long history of cultivation. However, studies on the characteristics among chloroplast (cp) genomes and the phylogenetic relationships of different mango varieties are still limited. To fill this research gap, we assembled, annotated, and compared the cp genomes of 23 mango germplasms. The mango cp genome exhibited a typical quadripartite structure, ranging in length from 157,604 to 158,949 bp. Each sequence encoded 129 genes, including 84 protein‐coding genes, 37 tRNA genes, and 8 rRNA genes. Nucleotide diversity analysis identified three mutation hotspot regions, trnH‐GUG‐psbA, ycf4‐cemA, and ndhF‐rpl32, which could be used to develop chloroplast‐specific markers. Phylogenetic analysis revealed that mango germplasm can be divided into four major clades, with wild and cultivated varieties forming independent clades. Interestingly, comparative chloroplast genomics and phylogenetics revealed a relatively low rate of genetic variation among cultivated mangoes. This phenomenon may be attributed to extensive interspecific hybridization and gene introgression events during mango domestication. This study provides valuable genomic resources for crop breeding and enhances our understanding of the genetic variation and phylogenetic relationships among different mango varieties. Three highly variable sites were identified as chloroplast‐specific markers. Low rate of genetic variation in the mango chloroplast genome. Gene introgression and hybridization affect the mango genetic diversity.

Malus sieversii (Rosaceae), a wild apple tree occurred in China's Xinjiang province, is considered to be the ancestor of the modern cultivated apple. However, information on the chloroplast (cp) genome of this species is limited. With this study, we produced the first cp genome of M. sieversii using genome skimming. The whole cp genome was 163,230 bp long and comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The M. sieversii cp genome had a GC content of 35.6%. Phylogenetic analysis showed that M. sieversii was deeply nested within the Malus clade. This study will be useful for future studies on conservation genetics and potential applications in apple breeding.

The Siberian flying squirrel (Pteromys volans) is an arboreal, nocturnal and gliding rodent. Due to irrational forest logging, its survival has been threatened. It is an urgent need to further evaluate the genetic changes of the population, especially the genetic diversity and inbreeding decline, so as to enhance the pertinence of conservation and management. We used microsatellite markers, to conduct genetic diversity analyses of four Siberian flying squirrel populations in southern Heilongjiang Province. Based on eight microsatellite loci, we found that the mean number of alleles was 12.9 (12.0 – 14.4) , the effective number of alleles was 8.6 (8.1 – 8.8) , the average observed heterozygosity was 0.887 (0.832 – 0.925) , the average expected heterozygosity was 0.872 (0.865 – 0.876) , and the inbreeding coefficient was -0.018 (-0.066 to 0.046) in the populations. Our results indicated a high level of genetic diversity in the Siberian flying squirrel populations, among which the Weihe population was the highes