Comparative de novo transcriptome analysis of male and female Sea buckthorn

Abstract

Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE (), phytochrome-associated serine/threonine-protein phosphatase (), protein TOPLESS (), sensitive to freezing 6 (), lysine-specific histone demethylase 1 homolog 1 (), pre-mRNA-processing-splicing factor 8A (), sucrose synthase 4 (), ubiquitin carboxyl-terminal hydrolase 12 (), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.

Transcriptome Sequencing and Analysis of Seabuckthorn (Hippophae Sp.)

“…The general steps in RNA-Seq bioinformatics analysis (Fig. 11.1b) (Fatima et al 2012a;Ghangal et al 2013;Bansal et al 2018;Ye et al 2018). However, despite the advancement in sequencing techniques and bioinformatics efficient tools, there were challenges in generating and analyzing seabuckthorn transcriptome data.…”

“…Recognizing males and females efficiently at an early stage is therefore essential for successful breeding programs in seabuckthorn. Toward this goal, an NGS-based comparative transcriptome study between male and female flower buds was conducted in seabuckthorn (Table 11.1) (Bansal et al 2018). In the study, author employed highthroughput RNA-Seq technique to understand the underlying molecular mechanism and gene involved in seabuckthorn sex determination.…”

“…The transcriptomic data generated from the female and male flower buds in the study by Bansal et al (2018) is publicly available at http:// www.bioinfoindia.org/sbt. The DEGs identified in the study provide new insight into the molecular mechanism involved in flowering and sex determination stages in seabuckthorn.…”

“…Illumina sequencing is widely used for several transcriptomes and genome-wide studies in different organisms. In seabuckthorn, most of the NGSbased transcriptome studies are conducted on the Illumina HiSeq platform (Ghangal et al 2013;Chaudhary and Sharma 2015;Bansal et al 2018;Ye et al 2018;Zhang et al 2018;Ding et al 2019). The Illumina HiSeq has many advantages over other sequencing platforms including the ability to generate a large number of short reads which helps in the accurate quantification of genome-wide steady-state RNAs.…”

Draft genome sequence of plastic degrading Bacillus sp. AIIW2 isolated from the Arabian ocean

“…The de novo genome identification and draft genome preparation had been done through the Medusa tool [16] using Bacillus sonorensis SRCM101395 as a reference genome for finishing. The primary genome assembly and secondary scaffolding were done through de novo genomic assembler Velvet v1.2.10 and SSPACE v3.0 [17,18], respectively. Plas-midFinder (V1.3) [19] and PHASTER tools [20] were applied for the presence of plasmid and bacteriophage sequences, respectively.…”