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The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

Tainia dunnii is a terrestrial orchid with high ornamental value. Herein, we assembled the complete chloroplast genome of Tainia dunnii by next-generation sequencing technologies. The compl...

Tainia cordifolia is a subtropical plant with significant ornamental value. Herein, we determined the complete chloroplast (cp) genome sequence of T. cordifolia using Illumina sequencing da...

Ludisia discolor is one of the most important ornamental and medicinal orchids. To improve our understanding of the evolution of chloroplast, we resequenced complete chloroplast (cp) genome of L. d...

Eria corneri is a perennial epiphytic orchid distributed in southeastern China with high value of ornamental and medicinal. In this study, the complete chloroplast genome sequence of E. corneri was determined from Illumina pair-end sequencing data. The complete chloroplast genome sequence of E. corneri is 150,538 base pairs (bp) in length, including one large single-copy region (LSC, 85,941 bp), one small single-copy region (SSC, 13,099 bp), and a pair of inverted repeat regions (IRs) of 25,749 bp. Besides, the complete chloroplast genome contains 132 genes, including 77 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that E. corneri was most closely related to Calanthe triplicata and Calanthe davidii. Our study provides a foundation for the identification and genotyping of Eria species.

Goodyera foliosa is a terrestrial orchid in Asia and has been listed as an endangered species in the Red List. In this study, we assembled the complete chloroplast genome of G. foliosa using Illumina sequencing data. Its full-length of 154,008 bp including a pair of invert repeats (IR) regions of 25,045 bp, large single-copy (LSC) region of 83,248 bp, and small single-copy (SSC) region of 20,670 bp. The chloroplast genome contains 127 genes, including 80 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis base on 12 chloroplast genomes of Orchidaceae indicates that G. schlechtendaliana is closely related to G. foliosa. Our study would be helpful for the formulation of conservation strategies and further research of G. foliosa.

Habenaria ciliolaris is a kind of orchid with ornamental value. In this study, we reported the complete chloroplast genome of H. ciliolaris. The complete chloroplast genome is 154,544 bp in length, consists of a pair of inverted repeat (IR, 25,455 bp) regions, a large single-copy region (LSC, 84,032 bp) and a small single-copy region (SSC, 19,602 bp). It contains 179 genes, including 133 protein-coding genes, 38 tRNAs, and 8 rRNAs. A maximum-likelihood phylogenetic analysis demonstrated a close relationship between H. ciliolaris and Habenaria radiata. This work will be valuable for genetic and phylogenetic studies on H. ciliolaris.

Cymbidium floribundum var. pumilum is an epiphytic orchid distributed in the southern China. It has a high ornamental value and always be used as a hybrid parent. In this study, we obtained a complete chloroplast genome of C. floribundum var. pumilum from BGISEQ-500 sequencing data. The total chloroplast genome was 155,291 bp in length, consisting of a large single copy region (LSC 84,415 bp), a small single copy region (SSC 17,484 bp), and two inverted repeat regions (IRA and IRB 26,696 bp). The complete chloroplast genome contains 139 genes, including 80 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. In addition, the phylogenetic analysis indicates that C. floribundum var. pumilum was sister to section Geocymbidium, section Pachyrhizanthe and section Jensoa. The chloroplast genome will contribute to establish an effective conservation strategy for C. floribundum var. pumilum.