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Transcriptome deep sequencing to reveal the gene regulation of variegated mutation in Phalaenopsis aphrodite subsp. formosana

ABSTRACT: Phalaenopsis aprodite subsp. formosana is one of the most important species for Phalaenopsis breeding. A mutant line with variegated leaf is found in this species. The green leaves bear unstable yellow sectors. In order to investigate the molecular mechanism of the variegated mutant line, we sequenced the transcriptome of variegated mutant by Illumina's Solexa sequencing technology. The sequence analysis results showed 22,598 unigenes by de novo assembly method, and the average unigene length was 1,286 bp. The bioinformatics tools were used to screen the differential expression between green and yellow sectors of leaves. There were 389 differentially expressed unigenes were identified. In addition, Gene ontology (GO) and KEGG pathway analyses revealed diverse biological functions and processes from differentially expressed genes. In transcriptome analysis, seven differential expression gene between the green and yellow sectors of leaves can be identified as CHLM, CRD1, POR, CLH, SGR, psbA and Lhcb6 by RNA deep sequencing. The expression of candidate genes was confirmed using semi-quantitative reverse transcription (RT) PCR and real-time RT PCR. The result showed that the significantly differential expression of CLH and SGR between green and yellow sectors was confirmed. It is suggested that the overexpressed SGR gene promotes the function of chlorophyllase, leading to the rapid degradation of chlorophyll in yellow sector. It causes the chlorophyll to not accumulate in the yellow sector, as a result, the variegated leaves are shown.

ORGANISM(S): Phalaenopsis aphrodite subsp. formosana

PROVIDER: GSE73123 | GEO | 2018/07/01

REPOSITORIES: GEO

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Project description:The yellow variegated2 (var2) mutant in Arabidopsis thaliana has been studied as a typical leaf-variegated mutant whose defect results from the lack of FtsH2 metalloprotease in chloroplasts. The var2 green sectors suffer from photooxidative stress and accumulate high levels of reactive oxygen species (ROS) because of compromised Photosystem II repair. This study investigated and compared microarray-based expression profiles of green and white sectors of var2 leaves. Results suggest that ROS that accumulate in chloroplasts of var2 green sectors do not cause much significant change of the transcriptional profile related to ROS signaling and scavenging. In contrast, transcriptome in white sectors apparently differs from those in green sectors and wild type. Numerous genes related to photosynthesis and chloroplast functions were repressed in white sectors. Furthermore, many genes related to oxidative stress were up-regulated. Among them, we specifically examined ROS scavenging genes, such as Cu/Zn superoxide dismutase 2 (CSD2), that were apparently up-regulated in white but not in green sectors. Up-regulation of CSD2 appears to be partly attributable to the lack of a microRNA (miR398) in white sectors. Together, we concluded that white sectors exhibit response to oxidative and other stresses, including CSD2 up-regulation, which might be commonly found in tissues with abnormal chloroplast differentiation. Arabidopsis thaliana ecotype Columbia (Col), used as the wild-type, and var2-1 (var2) were grown in MS medium supplemented with Gamborgâ??s vitamins (Sigma-Aldrich). MS medium was supplemented with 1.5% (w/v) sucrose and 0.7% (w/v) agar. Plants were maintained under a 12 h light (70 Î¼molâ?¢m-2â?¢s-1)/12 h dark cycle at 22Â°C. Green and white sectors, surgically separated and collected from 4-week-old true leaves were subjected to total RNA extraction. We also extracted total RNA from Col. Three biological replicates were performed for each sample.

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Transcriptome deep sequencing to reveal the gene regulation of variegated mutation in Phalaenopsis aphrodite subsp. formosana

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