Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.)

Satya, Pratik; Chakraborty, Avrajit; Sarkar, Debabrata; Karan, Maya; Das, Debajeet; Mandal, Nur Alam; Saha, Dipnarayan; Datta, Subhojit; Ray, Soham; Kar, C. S.; Karmakar, P. G.; Mitra, Jiban; Singh, Nagendra

doi:10.1016/j.phytochem.2018.08.017

Cited by 8 publications

(4 citation statements)

References 68 publications

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“…In addition, it is of great significance to study secondary cell wall (SCW) biosynthesis and promote the innovation of germplasm resources to study the expression and function of genes related to SCW and fibre quality. Transcription factors, such as MYB, WRKY and NAC, play an important role in the regulatory network of SCW biosynthesis (Chakraborty et al ., 2015; Samanta et al ., 2015; Satya et al ., 2018; Yang et al ., 2020). They can improve the fibre quality of plants by activating or inhibiting the expression of downstream genes.…”

Section: Introductionmentioning

confidence: 99%

Reference genomes of the two cultivated jute species

Zhang

et al. 2021

Plant Biotechnology Journal

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Summary Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

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Section: Introductionmentioning

confidence: 99%

Reference genomes of the two cultivated jute species

Zhang

et al. 2021

Plant Biotechnology Journal

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“…In flax, among the proteins with the Glyco_hydro_35 (PF01301) domain, the main catalytic domain of GH-35 β-galactosidases, only a portion also had the PF02140 domain (24 out of 43). Similarly, this was observed in jute (only six out of 11 β-galactosidases had galactose-binding lectin domains; Satya et al, 2018), tomato, and A. thaliana (12 out of 17 and 10 out of 17, respectively; Chandrasekar and van der Hoorn, 2016), while the lectin domain was present in all 17 β-galactosidases detected in peach (Guo et al, 2018). The β-galactosidases (Lus10028848 and Lus10008974) that are known as key players in the tertiary cell wall structure of flax fibers (Roach et al, 2011;Gorshkova et al, 2018a) are devoid of the PF02140 domain.…”

Section: Differentially Expressed Flax Lectins Between Samples With Distinct Cell Wall Typesmentioning

confidence: 70%

Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

et al. 2021

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The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

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“…The gene identification and pathway characterization studies were performed using stringent e-values (expect value, E < 10 − 5 ) following the BLAST program guideline. Gene expression (3 replicates) was compared using relative gene expression over the control using Pfaffl's "E-method" [36]. The results of HPLC analysis (4 replicates) are presented as the mean ± SD (SEM, 95 %).…”

Section: Discussionmentioning

confidence: 99%

“…Bast transcriptome of C. capsularis cv. JRC-212 (DDBJ/EMBL/Gen-Bank accession: GBSD00000000.1), as characterized earlier [35], was used to identify the unigenes encoding the FBP enzymes followed by their validation using its corresponding hypocotyl transcriptome (DDBJ/EMBL/GenBank accession: GCNR00000000.1) [36]. Corresponding genomic regions were identified from C. capsularis cv.…”

Section: Gene Identification and Pathway Constructionmentioning

confidence: 99%

Biosynthesis and Chemopreventive Potential of Jute (Corchorus capsularis and C. olitorius) Flavonoids and Phylogeny of Flavonoid Biosynthesis Pathways

Satya

Sarkar

Chatterjee

et al. 2022

Planta Medica International Open

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Flavonoids are valuable phytochemicals for human health and nutrition. Jute (Corchorus capsularis and C. olitorius), a vegetable rich in phenolics and flavonoids, is globally consumed for its health benefit, but the biosynthesis pathways and metabolic profiles of its flavonoids are poorly characterized. Elucidating the flavonoid biosynthesis pathways would augment the broader use of jute, including targeted synthesis of its specific flavonoids. We reconstructed the core flavonoid biosynthesis pathways in jute by integrating transcriptome mining, HPLC and flavonoid histochemistry. In C. capsularis (white jute), the flavonoid biosynthesis pathways’ metabolic flux was driven toward the biosynthesis of proanthocyanidins that mediate the acquisition of abiotic stress tolerance. However, higher levels of flavonols in C. olitorius (tossa jute) render it more suitable for nutritional and medicinal use. Jute flavonoid extract exhibited in vitro inhibition of matrix metalloproteinase-2, suggesting its potential chemopreventive and immunity-boosting roles. Using the flavonoid biosynthesis pathways profiles of 93 plant species, we reconstructed the flavonoid biosynthesis pathways phylogeny based on distance-based clustering of reaction paths. This reaction-path flavonoid biosynthesis pathways phylogeny was quite distinct from that reconstructed using individual gene sequences. Our flavonoid biosynthesis pathways-based classification of flavonoid groups corroborates well with their chemical evolution, suggesting complex, adaptive evolution of flavonoid biosynthesis pathways, particularly in higher plants.

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Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.)

Cited by 8 publications

References 68 publications

Reference genomes of the two cultivated jute species

Reference genomes of the two cultivated jute species

Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

Biosynthesis and Chemopreventive Potential of Jute (Corchorus capsularis and C. olitorius) Flavonoids and Phylogeny of Flavonoid Biosynthesis Pathways

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