Transcriptomic signature reveals mechanism of flower bud distortion in witches’-broom disease of soybean (Glycine max)

Abstract

BackgroundSoybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches’ broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways.ResultsWe report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD.ConclusionsThis is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1601-1) contains supplementary material, which is available to authorized users.

Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web‐genomic resource

“…Also, the maximum numbers of transcripts fall in the range of 200 to 299 bp as in a similar study (Hao et al, 2016). The comparison of reads mapped at 75, 90, and 95% similarity thresholds with < 5% variation align with previous studies, indicating that our transcriptome assembly is precise and the coverage/depth is uniform (Jaiswal et al, 2019). Black pepper is reported to have 63,466 protein‐coding genes (Hu et al, 2019).…”

Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]

“…Transcriptome sequencing or RNA-seq surpasses cloning and is helpful in exploring the complexity of transcriptome by allowing RNA analysis through cDNA sequencing at massive scale 49 . It has the potential to identify important secondary metabolic pathways, various transcripts associated with diseases and helpful for discovering novel genes 50 and developing molecular markers 51 . RNA sequencing (RNA-Seq) is widely used among the different transcriptome analysis methods as it can efficiently detect unknown genes and novel transcripts and has much potential to study gene expression and their regulating pathways 52 .…”

Stage Specific Comparative Transcriptomic Analysis to Reveal Gene Networks Regulating Iron and Zinc Content in Pearl Millet [Pennisetum Glaucum (L.) R. Br.]

“…Transcriptome sequencing or RNA-seq surpasses cloning and is helpful in exploring the complexity of transcriptome by allowing RNA analysis through cDNA sequencing at massive scale [52]. It has the potential to identify important secondary metabolic pathways, various transcripts associated with diseases and helpful for discovering novel genes [53] and developing molecular markers [54]. RNA sequencing (RNA-Seq) is widely used among the different transcriptome analysis methods as it can e ciently detect unknown genes and novel transcripts and has much potential to study gene expression and their regulating pathways [55].…”