The Sapotaceae family comprises 65–70 genera and over 1250 species, holding significant ecological and economic value. Although previous studies have made some progress in the phylogenetic relationships and classification of Sapotaceae, many issues remain unresolved and require further in-depth research. In this study, we sequenced and assembled the complete chloroplast genomes of 21 plants from 11 genera of Sapotaceae, conducted a comparative genomic analysis, and performed a phylogenetic analysis by incorporating 16 previously published chloroplast genomes of Sapotaceae. The results showed that the chloroplast genome sizes in 21 plants of Sapotaceae range between 157,920 bp and 160,130 bp, exhibiting the typical quadripartite structure. Each genome contains 84–85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, while the ndhF gene is absent in Pouteria campechiana and Pouteria sapota. The relative synonymous codon usage (RSCU) analysis showed that isoleucine (Ile) is the most commonly used, while the codon for methionine (Met) is the least utilized. Additionally, five highly variable regions (petA-psbJ, psbI-trnS-GGA, rpl2_2-psbA, rps19-rpl2_2, and ycf4-cemA) and two coding sequences, ycf1 and matK, were identified as candidate molecular markers for species differentiation and a phylogenetic analysis within the Sapotaceae family. Phylogenetic trees were reconstructed using complete chloroplast genome sequences and analyzed using ML and BI methods, which revealed that the Sapotaceae family is divided into three distinct clades, each receiving strong statistical support (BS = 100, PP = 1). The intergeneric analysis revealed that Madhuca and Palaquium are sister groups (BS = 91, PP = 1), as are Gambeya and Chrysophyllum (BS = 91, PP = 1). Pouteria and Chrysophyllum are among the larger groups in the Sapotaceae family but the traditional classification boundaries of these genera are unstable and unfeasible, as the current genus boundaries fail to support their natural evolutionary relationships. In the phylogenetic tree, Eberhardtia aurata is placed on a separate branch. The morphological classification system shows that E. aurata has rust-colored pubescence on its branches, abaxial leaf surfaces, petioles, and other areas, which clearly distinguishes it from other genera. This study provides valuable insights into advancing phylogenetic research, population genetics, molecular breeding, and conservation strategies by comparing chloroplast genome structures and characteristics and constructing phylogenetic trees.

Background: Salinity is a major environmental limiting factor, which affect agricultural production. The two Manilkara seedlings (M. roxburghiana and M. zapota) with high economic importance, could not adapt well to higher soil salinity and little is known about their proteomic mechanisms. Objectives: The mechanisms responsible for the effects of salinity on the two Manilkara species leaves were examined by means of proteomic analysis. Material and Methods: The seedlings were cultivated in a greenhouse and treated with NaCl. Leaves of control and the salt-stressed seedlings were sampled for phenol protein extraction. Proteins were separated by two-dimensional gel electrophoresis coupled with mass spectroscopy to study the change of proteins under different NaCl concentration. Results: For M. roxburghiana leaves, 21 protein spots exhibited significant abundance variations between the control and the 6‰, 8‰ NaCl treatments, of these 13 proteins were identified. They included L-ascorbate peroxidase, chloroplast carbonic anhydrase, phosphoglycerate kinase, 5 heat-shock proteins(HSPs) which were all down-regulated; For M. zapota leaves, 35 protein spots exhibited significant abundance variations, then 24 proteins were identified, including 7 down-regulated HSPs as well as glyceraldehyde-3-phosphate dehydrogenase, Cell division protein, putative mitochondrial NAD-dependent malate dehydrogenase, ATP synthase, Rubisco large subunit-binding protein, Cytochrome c peroxidase. Conclusions: Based on the common identified proteins between the two M. species, our results indicated that the identificated proteins in the two Manilkara species were involved in carbohydrate metabolism, photosynthesis, defense and stress. HSPs exhibited variation strictly related to NaCl stress. The down-regulated HSPs meant the function to repair cells that have suffered damage weaken during stress process. Furthermore, except for HSP70 in M. zapota leaves, the HSPs in the two species were all small heat shock proteins (sHSPs) with molecular weights ranging from 15 to 42 kDa. Iranian Journal of Biotechnology (IJB)