Abstract
Leaf color is an important agronomic trait in flowering plants, including orchids. However, factors underlying leaf phenotypes in plants remain largely unclear. A mutant displaying yellow leaves was obtained by the γ-ray-based mutagenesis of a Cymbidium orchid and characterized using RNA sequencing. A total of 144,918 unigenes obtained from over 25 million reads were assigned to 22 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, gene ontology was used to classify the predicted functions of transcripts into 73 functional groups. The RNA sequencing analysis identified 2,267 differentially expressed genes between wild-type and mutant Cymbidium sp. Genes involved in the chlorophyll biosynthesis and degradation, as well as ion transport, were identified and assayed for their expression levels in wild-type and mutant plants using quantitative real-time profiling. No critical expression changes were detected in genes involved in chlorophyll biosynthesis. In contrast, seven genes involved in ion transport, including two metal ion transporters, were down-regulated, and chlorophyllase 2, associated with chlorophyll degradation, was up-regulated. Together, these results suggest that alterations in chlorophyll metabolism and/or ion transport might contribute to leaf color in Cymbidium orchids.
Highlights
Orchids such as Cymbidium, Dendrobium, Oncidium, and Phalaenopsis are important cash crops worldwide, and the orchid industry has contributed substantially to the economy of many Southeast Asian countries [1, 2]
false discovery rate (FDR) 0.001367 0.014623 1.45 × 10−11 0.000628 0.009691 0.018302 0.010401 1.8 × 10−17 8.95 × 10−5 2.93 × 10−8 2.67 × 10−7 0.032332 7.76 × 10−13 0.006663 0.382536 0.787932 0.092632 0.491924 0.002168 transporter genes were ~4.5–52.3-fold higher in the S12 mutants (Fig 10J–10N). These results suggest that the reduced levels of Chl in the S12 mutant could be a result of increased Chl degradation and/or impaired ion transport associated with Chl biosynthesis
These results are consistent with a previous study [57], which suggested that the yellow-striped leaves of C. sinense variants were associated with increased Chl degradation
Summary
Orchids such as Cymbidium, Dendrobium, Oncidium, and Phalaenopsis are important cash crops worldwide, and the orchid industry has contributed substantially to the economy of many Southeast Asian countries [1, 2]. The biological significance and bio-diversity of genome sizes in angiosperms have received considerable attention in recent years [10, 11], the genomic organization of Orchidaceae remains poorly characterized. This could be largely owing to the poor genome representation of Orchidaceae, which contains over 28,000 species distributed in 763 genera [12]. The genomes of four orchids, Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen, have been sequenced [13]. The assembled sequenced genomes of orchids have predicted gene numbers ranging from 28,910 in P. equestris to 35,567 in D. officinale [15, 16]
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