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Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report the chloroplast genome sequence of Taeniophyllum complanatum, including an extensive comparative analysis with other types of leafless orchids. The chloroplast genome of T. complanatum exhibited a typical quadripartite structure, and its overall structure and gene content were relatively conserved. The entire chloroplast genome was 141,174 bp in length, making it the smallest known chloroplast genome of leafless epiphytic orchids. It encoded a total of 120 genes, including repetitive genes, comprising 74 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted on the chloroplast genomes of 43 species belonging to five subfamilies of Orchidaceae. The results showed that the five subfamilies were monophyly, with nearly all segments having a 100% bootstrap value. T. complanatum and Chiloschista were clustered together as a sister group to Phalaenopsis and occupied the highest position in the Epidendroideae. Phylogenetic analysis suggested that T. complanatum and other leafless orchids within the Orchidaceae evolved independently. This study may provide the foundation for research on phylogenetic and structural diversity in leafless epiphytic orchids, thereby enhancing the resources available for chloroplast genome studies in Orchidaceae. [ABSTRACT FROM AUTHOR]

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of Paraphalaenopsis (P. labukensis, P. denevel, and P. laycockii 'Semi-alba') and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (psbM-trnDGUC, psbB, ccsA, trnKUUU, trnSGCU-trnGUCC, rps16-trnQUUG) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that Paraphalaenopsis was a clade of Aeridinae that was sister to the Holcoglossum-Vanda clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae. [ABSTRACT FROM AUTHOR]

Cymbidium maguanense is a valuable orchid endemic to China, with delicate smelling, ivory white flower, and showy yellow labellum. Herein, we reported the complete chloroplast genome of C. maguanense. This chloroplast genome was 156,530 bp in length. It presented a typical structure including a large single-copy region (LSC, 85,112 bp), a small single-copy region (SSC, 17,874 bp), and two inverted repeat regions (IRs, 26,772 bp). It contained 138 genes, 37 tRNA, and 8 rRNA with an average GC content of 36.8%. Besides, the phylogenetic analysis showed that C. maguanense displayed a closer kinship to C. eburneum in the section Eburnea under subgenus Cymbidium. This chloroplast genome will provide a reference for future studies on species evolution, germplasm resources utilization, and genetic engineering of genus Cymbidium. [ABSTRACT FROM AUTHOR]

Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as 'Near Threatened (NT)' by IUCN Red List of China. Herein, we report the complete chloroplast genome (cpDNA) sequence assembled from Illumina pair-end sequencing data. The complete chloroplast genome was 156,424 bp in length, which includes two inverted repeat regions (IRs) of 26,776 bp each, which were separated by a large single copy region (LSC) 85,900 bp and a small single copy region (SSC) 16,972 bp. The chloroplast genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content in the chloroplast genome of C. montana was 37.0%. The phylogenomic analysis showed that C. montana is sister to Barthea barthei. [ABSTRACT FROM AUTHOR]

The plant genus Melastoma of the family Melastomataceae is comprised of nine species and one variety in China. Melastoma dodecandrum is the only creeping species of this genus. Previous study has reported the complete chloroplast genome of M. dodecandrum from Guangzhou, China, but there may be some differences between plant populations from different regions. Herein, we reported the complete chloroplast genome of M. dodecandrum from Fuzhou, China, which was assembled from Pacbio and whole genome data was sequenced. The sequence has a circular molecular length of 156,598 bp and contained 129 genes. Phylogenetic analysis indicated that M. dodecandrum was closely related to M. candidum in Melastomataceae. The study aims to provide insights for the future studies on the differences in molecular evolution level between plant populations of M. dodecandrum and taxonomy of Melastoma. [ABSTRACT FROM AUTHOR]

Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (B. cochinchinensis). The complete chloroplast genome (cp) size of B. cochinchinensis was 156,005 bp in length, containing a pair of 26,812 bp inverted repeat (IR) regions, which were separated by a large single-copy region (LSC) 85,926 bp and a small single-copy (SSC) region 16,455 bp. The overall GC content of the genome was 37.0%. The whole genome contained 129 unique genes, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that B. cochinchinens was sister to Barthea barthei. The present study provided B. cochinchinensis genomic information that may be found useful in conservation and molecular phylogenetic studies on Blastus. [ABSTRACT FROM AUTHOR]

Melastoma dodecandrum is recognized as an ideal industrial subshrub in Melastoma with special characters, like medicinal component, edible fruits, bizarre heteromorphic stamen flowers. Because of strong tolerance to drought and poor land, now it is gradually domesticated into functional economic crops. These special development characters and reported abundant metabolites are suspected to have influence by the mitochondria. To get a better understand of this potential species, we first generated the circle mitochondrial genome with Pacbio-Illumina hybrid sequencing strategy. Finally, the 411,944 bp physical map of M. dodecandrum displayed a long intergenic region segmentation structure and from the comparison with other plant mitogenomes, we unveiled large-scale rearrangements of conserved genes caused by micro inversions. A new insight highlighted the lateral gene transfer from nuclear, chloroplast to mitochondrial genome, consistent fragments captured functional genes like Cytb6f. In the generalized analysis of energy and metabolism genes, we detected a loss of ccmFN and a repeat of cox1 in the whole mitogenome, making it contain relatively complete energy metabolic system. Abnormal selective pressure occurred among the genes in mitogenome and chloroplast, inferring different driving forces of selection existed in the transfer of organic and nuclear genetic materials from hybridization event. This manifested a phylogenetic conflict between the mitochondrial gene and chloroplast gene tree. Eventually, our newly assembled mitogenome will add the knowledge of general trends in mitogenome evolution within dicotyledons and lay solid foundation to the future industrial development. • The reference mitochondrial genome of Melastoma dodecandrum marked large-scale rearrangements of conserved genes and lateral gene transfer [ABSTRACT FROM AUTHOR]