De novo assembly and annotation of Caesalpinia bonducella L. seed transcriptome identifies key genes in the biosynthesis of bonducellin, a homoisoflavonoid.

Caesalpinia bonducella L. is a traditional medicinal plant containing a potential homoisoflavonoid, bonducellin, with therapeutic values against polycystic ovary syndrome, oxidative damage, pathogenic bacteria, irregular menstrual cycle, ovarian cancer and diabetes. Owing to the multi-therapeutic properties of bonducellin, knowledge of its biosynthetic pathway genes will help understand its regulatory mechanism and thus improve the yield. This study sequenced C. bonducella seed mRNA transcriptome to identify the genes in bonducellin biosynthesis. Before this, the presence of bonducellin in the seed samples was analysed by HPLC using the chemically synthesised bonducellin as the standard. Seven key genes encoding enzymes involved in the synthesis of bonducellin via the phenylpropanoid pathway were identified. The expression of selective genes from the bonducellin biosynthetic pathway was validated using qRT-PCR and comparable with RNA-Seq data. Here, we put forth the sequences of 67,560 genes from C. bonducella and highlight the bonducellin biosynthetic pathway genes.

Transcriptome analysis of five different tissues of bitter gourd (Momordica charantia L.) fruit identifies full-length genes involved in seed oil biosynthesis.

The bitter gourd seed oil, rich in conjugated fatty acids, has therapeutic value to treat cancer, obesity, and aging. It also has an industrial application as a drying agent. Despite its significance, genomics studies are limited, and the genes for seed oil biosynthesis are not fully understood. In this study, we assembled the fruit transcriptome of bitter gourd using 254.5 million reads (Phred score > 30) from the green rind, white rind, pulp, immature seeds, and mature seeds. It consisted of 125,566 transcripts with N50 value 2,751 bp, mean length 960 bp, and 84% completeness. Transcript assembly was validated by RT-PCR and qRT-PCR analysis of a few selected transcripts. The transcripts were annotated against the NCBI non-redundant database using the BLASTX tool (E-value < 1E-05). In gene ontology terms, 99,443, 86,681, and 82,954 transcripts were classified under biological process, molecular function, and cellular component. From the fruit transcriptome, we identified 26, 3, and 10 full-length genes coding for all the enzymes required for synthesizing fatty acids, conjugated fatty acids, and triacylglycerol. The transcriptome, transcripts with tissue-specific expression patterns, and the full-length identified from this study will serve as an important genomics resource for this important medicinal plant.

The complete chloroplast genome of Ocimum gratissimum from India - a medicinal plant in the Lamiaceae.

Ocimum gratissimum L. is an important medicinal species with several therapeutic applications. It is used in traditional medicine as a single drug and in formulations. We generated the complete chloroplast genome sequence of O. gratissimum by using Illumina paired-end sequencing data. The O. gratissimum chloroplast genome is 152,469 bp in length, containing a large single copy (LSC) region of 83,614 bp and a small single copy region (SSC) of 17,607 bp, separated by a pair of inverted repeats (IRs) of 25,624 bp. The genome contains 138 unique genes, including 85 protein-coding, 45 tRNA, and eight rRNA genes. Among them, six genes have one intron each, and two genes contain two introns. The overall GC content of the chloroplast genome is 37.8%, while the corresponding values of LSC, SSC, and IR regions are 35.6%, 31.7%, and 43.2%, respectively. Phylogenetic analysis with the complete chloroplast genomes of other related species revealed that O. gratissimum is fully resolved in a clade with other Ocimum species classified to the family Lamiaceae.