De novo-based transcriptome profiling of male-sterile and fertile watermelon lines

Rhee, Sun-Ju; Kwon, Tae-Hyung; Seo, Minseok; Jang, Yoon Jeong; Sim, Tae Yong; Cho, Seoae; Han, Sang-Wook; Lee, Gung Pyo

doi:10.1371/journal.pone.0187147

Cited by 8 publications

(4 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The expression patterns of GRAS genes in various tissues, including roots, stems, leaves, flowers, and fruits, were analyzed utilizing publicly available RNA-seq data [36,[51][52][53][54][55][56][57][58]. The RNA-seq data were processed using Hisat2 (version: 2.1.0) [59] to align to the six cucurbit plant genomes and assembled using StringTie (version: 1.3.4) [60].…”

Section: Rna-seq Analysis Of Gras Genes In Various Tissuesmentioning

confidence: 99%

Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

Zhang

Wang

et al. 2023

Horticulturae

View full text Add to dashboard Cite

The Cucurbitaceae family comprises economically valuable vegetables such as cucumber, melon, and pumpkin. GRAS proteins, which are crucial transcription factors, play diverse roles in plant growth and development. However, comparative investigations of GRAS proteins across Cucurbitaceae species are limited. Here, we identified 241 GRAS family genes in six cucurbit crops. The number of GRAS genes in cucumber, melon, wax gourd, watermelon, and bottle gourd ranged from 36 to 37, while the pumpkin genome contained 57 GRAS genes, possibly due to a recent whole-genome duplication. We classified cucurbit GRAS genes into 16 subfamilies and identified species-specific motifs and specific-expression patterns in the SCLB and RAD1 subfamilies. Notably, we identified 38 tissue-specific expressed genes, particularly fruit-specific genes potentially involved in fruit development. Additionally, we predicted the role of GRAS genes in regulating hypocotyl elongation under weak or dark light conditions in cucurbit plants. These findings enhance our understanding of the characteristics, evolution, and potential functions of GRAS genes in six cucurbit crops, providing valuable resources for genetic research in the Cucurbitaceae family as well as important agronomic traits.

show abstract

Section: Rna-seq Analysis Of Gras Genes In Various Tissuesmentioning

confidence: 99%

Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

Zhang

Wang

et al. 2023

Horticulturae

View full text Add to dashboard Cite

show abstract

“…We analyzed the expression pro les of GRAS genes in different tissues, including roots, stems, leaves, owers and fruits, using public RNA-seq data [26,[62][63][64][65][66][67][68]. RNA-seq data from ve tissues were mapped to the six Cucurbitaceae plant genomes using Hisat2 (version: 2.1.0) [69] with default settings for parameters and were assembled using stringtie (version: 1.3.4) [70].…”

Section: The Expression Of Gras Genes In Different Tissuesmentioning

confidence: 99%

Comparative analysis of GRAS genes in six Cucurbitaceae species provides novel insights into their evolution and function

Zhang

et al. 2021

Preprint

View full text Add to dashboard Cite

Background GRAS proteins are important transcription factors that play essential roles in diverse fundamental processes of plant growth and development. However, the features, evolution and potential functions of GRAS genes among the Cucurbit crops remain largely unknown. Results In this study, we identified 237 GRAS gene sequences from six Cucurbitaceae species. The genomes of Cucumis sativus L., Cucumis melo L., Benincasa hispida L., Citrullus lanatus L. and Lagenaria siceraria L. contain 35 to 37 GRAS genes, whereas 55 are present in Cucurbita moschata L. which should be derived from a recent whole genome duplication. These GRAS genes were divided into sixteen subfamilies on the basis of their phylogenetic relationships. In the SCLB and RAD1 subclade, three specific motifs were found in Cucurbitaceae species, implying the potential Cucurbitaceae-specific functions. Duplication and synteny analysis revealed that segmental and tandem duplication may be the main reasons for the expansion of the GRAS family in Cucurbitaceae species, and that whole-genome duplication is the main reason for the greater number of GRAS genes in Cucurbita moschata L.. Some GRAS genes exhibit tissue-specific, subfamily-specific or Cucurbitaceae-specific expression patterns, implying that they may play key roles in specific developmental processes in cucurbit crops. Conclusions This study provides insights into the features, evolution and potential functions of GRAS genes in Cucurbitaceae species, which may be associated with important agronomic traits.

show abstract

“…We previously conducted reference-and de novo RNA-seq to detect differentially expressed genes (DEGs) between the MS and MF lines of DAH3615 (Rhee et al, 2015;Rhee et al, 2017).…”

Section: Cfmmv-vigs Systemmentioning

confidence: 99%

“…(Figure 1). Putative male sterility-related genes were deduced from reference-based and de novo RNA-seq in male sterile and fertile watermelon lines previously reported by our group (Rhee et al, 2015;Rhee et al, 2017). pCF93-pds.int, constructed by inserting a partial fragment of pds intron into the MCS region of pCF93, was used as a mock.…”

Section: Cloning Of Target Insert Genes For Vigsmentioning

confidence: 99%

Induction of virus-induced gene silencing andin plantavalidation in cucurbits using the CFMMV-Cm vector

Lee

Rhee

Jang

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Virus-induced gene silencing (VIGS) has been employed for the high-throughput analysis of endogenous gene function. We developed a CaMV 35S promoter-driven cucumber fruit mottle mosaic virus-Cm vector (pCF93) for the efficient generation of viral transcripts in plants. Using the novel pCF93 vector, we identified genes related to male sterility in watermelon (Citrullus lanatus), which is recalcitrant to genetic transformation. We previously reported reference-based and de novo transcriptomic profiling for the detection of differentially expressed genes between a male fertile line (DAH3615) and its near isogenic male sterile line (DAH3615-MS). Based on the RNA-seq results, we identified 38 de novo-exclusive differentially expressed genes (DEDEGs) that are potentially responsible for male sterility. Partial genes of 200∼300bp were cloned into pCF93 which was then inoculated into DAH, a small type of watermelon that enables high-throughput screening with a small cultivation area. In this manner, we simultaneously characterized phenotypes associated with the 38 candidate genes in a common-sized greenhouse. Eight out of the 38 gene-silenced plants produced male sterile flowers with abnormal stamens and no pollens. Gene expression levels in flowers were validated via RT-qPCR. Stamen histological sections from male sterile floral buds and mature flowers showed developmental disruption and shrunken pollen sacs. Based on the current findings, we believe that the novel pCF93 vector and our VIGS system facilitate high-throughput analysis for the study of gene function in watermelons.One sentence summaryThe CaMV 35S promoter-driven cucumber fruit mottle mosaic virus-Cm vector (pCF93) facilitates large-scale validation of male sterility-related gene functions in watermelon.

show abstract

De novo-based transcriptome profiling of male-sterile and fertile watermelon lines

Cited by 8 publications

References 55 publications

Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

Comparative analysis of GRAS genes in six Cucurbitaceae species provides novel insights into their evolution and function

Induction of virus-induced gene silencing andin plantavalidation in cucurbits using the CFMMV-Cm vector

Contact Info

Product

Resources

About