Transcriptome profiling as a means to provide molecular evidence for the decline of tree bean (Parkia Roxburghii G. Don) and the creation of its web-genomic resource

The tree bean, Parkia roxburghii G. Don, is a lesser-known, yet nutrient-dense, leguminous tree that grows luxuriantly in northeastern (NE) India and southeast Asia. It belongs to the family Fabaceae (previously, Leguminosae). The tree bean, specifically in Northeast India, is experiencing serious challenges due to signs of decline. This issue manifests as partial twig drying, which eventually dries out half to three-quarters of the tree, leaf falling and yellowing, gummosis, insect excreta etc. This has led to a significant loss of this plant in major part of the northeastern states of India. To identify key genes responsible for the decline of the plant, tissues from the declining and healthy plants were collected in triplicate for transcriptome analysis and sequenced using the Illumina platform, generating approximately 31 GB of paired end reads. A total of 286 differentially expressed genes (DEGs) (119 upregulated and 167 downregulated) were obtained at log2FC ± 2 and FDR 0.05. Among the upregulated transcripts, most of them were related to stress response. In contrast, for downregulated transcripts, DEGs were related to abscission, cell death, pathogen response, oxidative stress response, reduced in cuticular wax synthesis etc. We also mined 81,482 and 321 SSR markers from de novo transcriptome assembly and DEGs, respectively, with the abundance of trinucleotide and mononucleotide repeats. Also, 180,092 variants were discovered in decline and healthy samples, along with 39 transcription factor family proteins and 1889 mature miRNA targets. With this information, we developed the first comprehensive and user-friendly web genomic resource, ParkRoxTDB for tree bean, accessible at https://parkroxtdb.daasbioinfromaticsteam.in/ . This study gives us insight into the molecular processes that are differentially expressed in the decline and healthy tree bean trees. The web resource will play an important role in tree bean improvement and management programs, QTL mapping, diversity analysis, and evolutionary studies.