Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn (Hippophae salicifolia)

Abstract

Seabuckthorn (Hippophae salicifolia) is a perennial, multipurpose wonder plant, popular for its immense medicinal, nutritional, and therapeutic properties. However, due to the lack of whole-genome-based studies, the molecular mechanism governing distinct sexual phenotypes is still not clear. We employed the high-throughput NGS Illumina NovaSeq paired-end technology to generate whole transcriptome profiles of male and female plants of H. salicifolia. In total, 3.2 million raw short reads were generated with an average length of 150 bp, including 50911358 reads from the male leaf tissue samples and 45850364 reads from the female leaf tissue samples. Clustering of the high-quality reads yielded de novo short read assembly of 50259 transcripts of >100 bp length. The final transcripts were assigned Gene Ontology (GO) terms. The digital expression of genes was studied using the DESeq2 of R package that identified 7180 differentially expressed genes (DEGs) between the male and female plant samples. Further, 10,850 simple sequence repeats, and 8,351 transcription factors, distributed in more than 85 transcription families, were also mined from the final assembled transcriptome. Next, COG and KEGG pathway analyses were performed to assign biological functional terms to the DEGs. The findings of the present study will provide a valuable resource for gene expression discovery and other functional genomics studies aiming towards the selection of candidate genes for the development of sex-specific markers in seabuckthorn and other closely related species.

Communicated by Ramaswamy H. Sarma

Keywords:

• Seabuckthorn
• Hippophae salicifolia
• Gender-based gene expression
• transcriptome sequencing
• transcription factors
• simple sequence repeats

Acknowledgments

We are grateful to Dr. Vijay Bhatt (Assistant Professor, Herbal Research and Development Institute, Gopeshwar, Chamoli, Uttarakhand) for providing seabuckthorn stem cutting saplings. PC also acknowledges for awarding an STRF (Short Term Research Fellowship).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Faculty Research Grant Scheme (GGSIPU/DRC/FRGS/2020/1988/20) of Guru Gobind Singh Indraprastha University, New Delhi, India.