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The aim of the study was to characterize the chloroplast genome structure and phylogenetic relationships within the genus Bulbophyllum. We sequenced, assembled, and annotated the chloroplast genomes of B. rothschildianum and B. longissimum for the first time. Comparative analyses of codon usage bias, repeat sequences, and sequence variation were then conducted with the available chloroplast genomes from four previously published Bulbophyllum species. The chloroplast genome of B. rothschildianum and B. longissimum was 148 447 bp and 151 095 bp, respectively, both showing a typical circular quadripartite structure containing 126 and 129 functional genes. Codons encoding leucine exhibited the strongest usage bias, with codons ending in A/U being particularly abundant. SSR analysis revealed mononucleotide repeats (predominantly A/T type) were most abundant, and palindromic repeats dominated among long repeats. Highly variable regions were mainly located in non-coding regions and selected coding genes (e.g., matK and ycf1), with evident expansion and contraction at IR/SC boundaries. Phylogenetic analysis showed that the 32 Bulbophyllum species formed a strongly supported clade and exhibited clear geographic differentiation into Asian and Central and South American lineages, with B. rothschildianum and B. longissimum clustering together within the Asian lineage and being closely related. The study would provide molecular insights into resource development, genetic conservation, and systematic research in the genus Bulbophyllum.
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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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