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Taking the chloroplast genomes of five coffea plants, namely Coffea liberica, C. canephora, C. arabica, C. eugenioides, and C. racemosa, as the research objects, a series of statistical and comparative analyses were carried out. The results demonstrated that the lengths of the chloroplast genomes varied from 154 751 bp to 155 189 bp, with C. arabica a possessing the longest genome and C. canephora having the shortest. The average GC content was determined to be 34.98%. Both C. liberica and C. arabica encoded 130 genes, while C. eugenioides had the largest number of genes, totaling 138, and C. racemosa had the least, with only 121. Upon comparing the border regions of the chloroplast genomes of the five coffee plants, it was observed that the directional sequence arrangements were consistent, thereby reflecting the high conservation of the chloroplast genome structure. The analysis of SSR sequences indicated that the five coffee plants exhibited a pronounced AT bias, and the types and quantities of SSRs differed among them. Through the analysis of nucleotide diversity variation sites, five segments with relatively significant nucleotide variations were identified, namely PetN-PsbM, accD, accD-PsaI, rpl16 and ndhF-rpl32. Furthermore, based on the combined analysis of the chloroplast genomes and the five highly variable nucleotide regions, a phylogenetic tree of 19 Coffea plants was successfully constructed, which shed light on their genetic relationships. This study can serve as a valuable reference for the identification of germplasm resources, the exploration of origin and evolution, as well as the hybrid breeding of Coffea plants.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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