Ye Ai’s research while affiliated with Fujian Agriculture and Forestry University and other places

Background Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.

Colorful leaves, particularly red ones, represent an important ornamental trait of Cymbidium ensifolium. However, the mechanisms underlying red leaf formation in C. ensifolium are not well understood. In this study, we examined the phenotypic, physiological, and transcriptomic differences between red and green leaves at various developmental stages. We found that red leaves exhibited significantly lower levels of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll across all stages, while anthocyanin levels were notably higher. Ultra-structural analysis revealed abnormalities in the chloroplast structure of red leaves, including fewer chloroplasts, ruptured thylakoid membranes, an indistinct matrix layer, and the accumulation of osmiophilic particles, which led to reduced photosynthetic capacity. In addition, transcriptomic analysis showed significant differences in the expression of genes related to anthocyanin biosynthesis, chlorophyll metabolism, and photosynthesis between red and green leaves at different stages of growth. Therefore, we suggest that red leaf formation in C. ensifolium is driven by reduced expression of chlorophyll metabolism genes, resulting in impaired chloroplast development and chlorophyll synthesis, while upregulation of anthocyanin biosynthesis genes promotes anthocyanin accumulation , leading to the red coloration. These findings provide valuable insights into color formation mechanisms of red leaves in C. ensifolium.

Background: Containing the largest number of species, the orchid family provides not only material for studying plant evolution and environmental adaptation, but also economically and culturally important ornamental plants for the human society. Previously, we collected genomic and transcriptomic information on Apostasia shenzhenica , Dendrobium catenatum , Phalaenopsis equestris , and two species of Platanthera that belong to three different subfamilies of Orchidaceae, and developed user-friendly tools to explore orchid genetic sequences in OrchidBase. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense , C. ensifolium and C. goeringii , were sequenced de novo , assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion: OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.

Terpene synthases (TPSs) are crucial for the diversification of terpenes, catalyzing the formation of a wide variety of terpenoid compounds. However, genome-wide systematic characterization of TPS genes in Cymbidium ensifolium has not been reported. Within the genomic database of C. ensifolium, we found 30 CeTPS genes for this investigation. CeTPS genes were irregularly distributed throughout the seven chromosomes and primarily expanded through tandem duplications. The CeTPS proteins were classified into three TPS subfamilies, including 17 TPS-b members, 8 TPS-a members, and 5 TPS-c members. Conserved motif analysis showed that most CeTPSs contained DDxxD and RRX8W motifs. Cis-element analysis of CeTPS gene promoters indicated regulation primarily by plant hormones and stress. Transcriptome analysis revealed that CeTPS1 and CeTPS18 had high expression in C. ensifolium flowers. qRT-PCR results showed that CeTPS1 and CeTPS18 were predominantly expressed during the flowering stage. Furthermore, CeTPS1 and CeTPS18 proteins were localized in the chloroplasts. These results lay the theoretical groundwork for future research on the functions of CeTPSs in terpenoid biosynthesis.

Cymbidium floribundum is an ornamental plant with showy and colorful flowers. The color of its lip changes significantly after pollination. However, the mechanism of lip coloration remains unclear. In this study, the mechanism underlying lip color change in C. floribundum was investigated before and after pollination. Metabolome analysis detected 61 flavonoids in the lip, including 24 flavonoids, 13 flavonols, nine flavonoid carbonosides, eight anthocyanins, three flavanols, two isoflavones, one chalcone, and one dihydroflavone. Accumulation of peonidin 3-O-glucoside chloride, cyanin chloride, and cyanidin 3-O-malonylhexoside after pollination may be the key factors contributing to the change in lip color. Furthermore, transcriptome analysis identified 43 genes related to the anthocyanin biosynthesis pathway (ABP). Phylogenetic and co-expression analysis indicated that CfMYB1, CfMYB3, and CfMYB4 may be involved in the regulation of anthocyanin biosynthesis in the lips. Subcellular localization results showed that CfMYB1 was located in the nucleus, while CfMYB3 and CfMYB4 were located in the nucleus and cytoplasm. Further functional analysis verified that CfMYB1 could activate ABP genes and promote the synthesis and accumulation of anthocyanin, which may be the main transcription factors leading to the change of lip color in C. floribundum after pollination. These findings provide insight into the anthocyanin accumulation and coloration mechanisms during C. floribundum flower development. The results provide genetic resources and a theoretical basis for the improvement and breeding of flower color in C. floribundum.

The PIN (PIN-formed) proteins act as vital carriers, regulating auxin polar transport and playing a crucial role in plant growth and development. Cymbidium ensifolium (Orchidaceae) is a perennial herbaceous plant highly esteemed for its high ornamental value. The lotus-shape flowers of C. ensifolium are favored by consumers for their distinctive flower shape with shorter petals. To deepen our understanding of the members and characteristics of PIN gene family in C. ensifolium, this study performed genome-wide identification and analysis of CePIN members, including their physicochemical properties, protein and gene structures, conserved motifs, phylogenetic evolution, promoter components, and expression patterns. The results revealed a total of 16 PIN gene family members in the genome of C. ensifolium. Expression analysis demonstrated significant differential expression of all 16 CePINs across different tissues. Notably, a close correlation was observed between the expression of CePIN1a and CePIN3 and the formation of lotus-shape flowers in C. ensifolium. These findings provide a foundational understanding for further exploration of CePIN functions and offer valuable insights for studying petal development in C. ensifolium.

The PEBP gene family is involved in many biological processes in plants, including plant growth and development, flowering regulation, light response, and abiotic stress response. But there is little information about the role of the PEBP gene family in Cymbidium species. In this study, we identified 11, 9, and 7 PEBP genes in C. ensifolium, C. sinense, and C. goeringii, respectively, and mapped them to the chromosomes. We also studied the physicochemical characteristics of the proteins encoded by these PEBPs and analyzed their intra-species collinearity, gene structure, conserved motifs, and cis-acting elements. Furthermore, a total of forty PEBP genes from C. sinense, C. ensifolium, C. goeringii, Phalaenopsis, and Arabidopsis were divided into three clades based on the phylogenetic tree. The expression patterns of 11 PEBP genes in different tissues and organs of C. ensifolium were analyzed based on transcriptome data, indicating that the CePEBPs might play an important role in the growth and development, especially in the flower bud organs (1–5 mm). CePEBP5 plays an indispensable role in both the vegetative and reproductive growth cycles of C. ensifolium. CePEBP1 is essential for root development, while CePEBP1, CePEBP3, CePEBP5, and CePEBP10 regulate the growth and development of different floral organ tissues at various stages. The findings of this study can do a great deal to understand the roles of the PEBP gene family in Cymbidium.

The basic leucine zipper (bZIP) transcription factors constitute the most widely distributed and conserved eukaryotic family. They play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses, exerting strong regulatory control over the expression of downstream genes. In this study, a genome-wide characterization of the CebZIP transcription factor family was conducted using bioinformatic analysis. Various aspects, including physicochemical properties, phylogenetics, conserved structural domains, gene structures, chromosomal distribution, gene covariance relationships, promoter cis-acting elements, and gene expression patterns, were thoroughly analyzed. A total of 70 CebZIP genes were identified from the C. ensifolium genome, and they were randomly distributed across 18 chromosomes. The phylogenetic tree clustered them into 11 subfamilies, each exhibiting complex gene structures and conserved motifs arranged in a specific order. Nineteen pairs of duplicated genes were identified among the 70 CebZIP genes, with sixteen pairs affected by purifying selection. Cis-acting elements analysis revealed a plethora of regulatory elements associated with stress response, plant hormones, and plant growth and development. Transcriptome and qRT-PCR results demonstrated that the expression of CebZIP genes was universally up-regulated under low temperature conditions. However, the expression patterns varied among different members. This study provides theoretical references for identifying key bZIP genes in C. ensifolium that confer resistance to low-temperature stress, and lays the groundwork for further research into their broader biological functions.

Cymbidium ensifolium is one of the national orchids in China, which has high ornamental value with changeable flower colors. To understand the formation mechanism of different flower colors of C. ensifolium, this research conducted tran-scriptome and metabolome analyses on four different colored sepals of C. ensifolium. Metabolome analysis detected 204 flavonoid metabolites, including 17 polyphenols, 27 anthocyanins, 75 flavones, 34 flavonols, 25 flavonoids, 18 flavanones, and 8 isoflavones. Among them, purple-red and red sepals contain a lot of anthocyanins, including cyanidin, pelargonin, and paeoniflorin, while yellow-green and white sepals have less anthocyanins detected, and their metabolites are mainly flavonols, flavanones and flavonoids. Transcriptome sequencing analysis showed that the expression levels of the anthocyanin biosynthetic enzyme genes in red and purple-red sepals were significantly higher than those in white and yellow-green sepals of C. ensifolium. The experimental results showed that CeF3′H2, CeDFR, CeANS, CeF3H and CeUFGT1 may be the key genes involved in anthocyanin production in C. ensifolium sepals, and CeMYB104 has been proved to play an important role in the flower color formation of C. ensifolium. The results of transformation showed that the CeMYB104 is involved in the synthesis of anthocyanins and can form a purple-red color in the white perianth of Phalaenopsis. These findings provide a theoretical reference to understand the formation mechanism of flower color in C. ensifolium. Key message This study identified the differential metabolites and differential genes among different color sepals, determined the key regulatory genes, and constructed a regulatory network for the flower color formation of Cymbidium ensifolium.

The basic helix-loop-helix (bHLH) transcription factors are widely distributed across eukaryotic kingdoms and participate in various physiological processes. To date, the bHLH family has been identified and functionally analyzed in many plants. However, systematic identification of bHLH transcription factors has yet to be reported in orchids. Here, 94 bHLH transcription factors were identified from the Cymbidium ensifolium genome and divided into 18 subfamilies. Most CebHLHs contain numerous cis-acting elements associated with abiotic stress responses and phytohormone responses. A total of 19 pairs of duplicated genes were found in the CebHLHs, of which 13 pairs were segmentally duplicated genes and six pairs were tandemly duplicated genes. Expression pattern analysis based on transcriptome data revealed that 84 CebHLHs were differentially expressed in four different color sepals, especially CebHLH13 and CebHLH75 of the S7 subfamily. The expression profiles of CebHLH13 and CebHLH75 in sepals, which are considered potential genes regulating anthocyanin biosynthesis, were confirmed through the qRT-PCR technique. Furthermore, subcellular localization results showed that CebHLH13 and CebHLH75 were located in the nucleus. This research lays a foundation for further exploration of the mechanism of CebHLHs in flower color formation.