Next generation sequencing and transcriptome analysis for identification of ARF and Aux/IAA in pointed gourd (Trichosanthes dioica Roxb.), a non-model plant

• Published in: Scientia horticulturae Vol. 301; p. 111152
• Main Authors: Saurabh, Satyajit, Prasad, Dinesh, Masi, Antonio, Vidyarthi, Ambarish S.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 27.07.2022
• Subjects: ARF; Auxin signaling; IAA; Pointed gourd; Transcriptome; Trichosanthes dioica Roxb; IAA; Pointed gourd; Auxin signaling; ARF; Trichosanthes dioica Roxb; Transcriptome
• ISSN: 0304-4238; 1879-1018
• DOI: 10.1016/j.scienta.2022.111152

•The next generation sequencing and comprehensive transcriptome analysis of the T. dioica Roxb. were performed for ovary samples of two different stages: the day before pollination (DBP) and the day after fertilization (DAF).•The BLAST-hits analysis of significantly annotated CDS of both samples revealed that pointed gourd is significantly related with cucumber (Cucumis sativus) having 79% and 77% similarity for DBP and DAF, respectively.•The analyses were performed for differentially expressed transcripts. A total of 10,996 annotated CDS was commonly identified in both samples. Notably, 1,859 CDS were found significantly down-regulated while 1,194 CDS were found up-regulated. These genes may be studied further for genetic regulations and physiological changes in different stages of ovary development and fruit set. The Simple Sequence Repeat (SSR) motifs were identified in 904 CDS of 1DBP and 971 CDS of 2DAF. Mostly, dimer and trimer SSR motifs were found in both samples.•This study has generated genetic resources for transcription factors, ARFs and IAAs, known primarily for regulating the auxin-dependent phenomenon in plant physiology. Significantly upregulated and downregulated ARF and IAA genes showed these genes play a vital role in ovary maturation and fruit development. Neighbour Joining analysis for the phylogenetic relationship of ARF and Aux/IAA gene families in T. dioica Roxb. and Arabidopsis thaliana revealed higher similarity.•The information gathered through these analyses will provide a better understanding to apply genetic tools for biotechnological interventions in this plant. The Pointed gourd (Trichosanthes dioica Roxb.) belonging to the family Cucurbitaceae is a tropical perennial vegetable with an origin in the Indian subcontinent. There is a lack of genetic information for this commercially important cucurbit. A comprehensive transcriptome analysis of the T. dioica Roxb. ovary was carried out in this study. The BLAST-hits analysis of significantly annotated CDS of both samples revealed that pointed gourd is significantly related to cucumber (Cucumis sativus). A total of 10,996 annotated CDS was commonly identified in both samples. Notably, 1,859 CDS were found significantly down-regulated while 1,194 CDS were found up-regulated. 904 CDS of 1DBP and 971 CDS of 2DAF were identified to have SSRs. The auxin-dependent phenomenon in plant physiology, auxin signaling, is primarily regulated by transcription factors, such as ARF and Aux/IAA. The in-silico studies were carried out to identify the transcripts of ARFs and IAAs in T. dioica Roxb. A total of 48 ARF transcripts and 37 Aux/IAA transcripts were identified and named as TdARFs and TdIAAs, respectively. The peptides of TdARFs and TdIAAs are distributed in clusters to show similarity and evolutionary divergence. More than 70% of the peptide sequences derived from CDS of TdARFs and TdIAAs have their signature domains. The sub-cellular localization predicted that TdARF and TdIAA were found mainly in the nucleus. This study will pave the way further for elucidating the precise role of these transcription factors in auxin signaling and subsequent genetic manipulations for crop improvement. Additionally, the data sets gathered from whole transcriptome sequencing and analysis are useful resources for further studies regarding molecular genetics and functional genomics of T. dioica Roxb. [Display omitted]