Selection of stable housekeeping genes for qPCR in biotic and abiotic stressed jute and their application in lignin pathway analysis

Parida, Subhadarshini; Datta, Swapan K.; Dey, Nirshingha; Majumder, Shuvobrata

doi:10.1016/j.stress.2024.100525

Cited by 1 publication

(1 citation statement)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The melt curve of the amplified PCR products was obtained from 60 ℃ to 95 ℃. The jute ubiquitin1 (UBI) gene (GenBank accession GH985256) was used as an internal control (Parida et al, 2024). The mRNA transcript expression levels were calculated and represented by relative quantification (RQ) values according to the method described by Livak and Schmittgen (2001).…”

Section: Gene Expression Analysis In Qrt-pcrmentioning

confidence: 99%

Genome-wide Identification of the Laccase Gene Family in White Jute (Corchorus capsularis): Potential Targets for Lignin Engineering in Bast Fiber

Parida,

Jha,

Kumari

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

The industrial bast fibre crop jute (Corchorussp.) is known for its long lignocellulosic multi-utility fibres. Information on jute fibre lignification is limited, and many enzymes in the jute lignin pathway are not well documented. One such enzyme is laccase (EC 1.10.3.2), involved in the final polymerization step of lignification. A whole-genome search of white jute (Corchorus capsularis) revealed 34 putative laccase (CcaLAC) genes. Phylogenetic analysis categorized these genes into six groups, with 17 predominantly expressed in phloem tissue, 9 in leaf, and 4 in xylem and roots. A steady increase in gene expression, from plantlets to crop harvest, was observed for severalCcaLACs. Some were selected for further analysis based on homology withArabidopsislignin pathway-modifying laccases (AtLACs). Transcriptomics data confirmed their expression in phloem tissues, with some showing significantly lower expression indlpf, a low-lignin fibre-containing white jute mutant. Changes inCcaLACexpression were observed under abiotic stresses like ABA hormone and copper heavy metal. Target sites for Ath-miR397a and Ath-miR397b were predicted in 11 and 9CcaLACs, respectively, suggesting possible post-transcriptional modification via microRNA. Subcellular localization showedCcaLACs in multiple plant cell compartments. Protein structure predictions revealed up to 10 motifs in CcaLACs, with 18 containing transmembrane helices. Overall,CcaLAC28andCcaLAC32are likely involved in the lignification process of phloem (bast) in white jute. Modifying these genes could enhance our understanding of lignification and potentially lead to the development of low-lignin jute fibres, meeting high industrial demands globally.HighlightsJute is known for its long lignocellulosic fibres.34 putative laccase genes were identified in white jute.17 laccase genes are mainly expressed in phloem tissue.CcaLAC28andCcaLAC32are key candidates for lignification.Laccase genes showed changes under abiotic stresses.Key MessageIdentified 34 laccase genes in white jute, key for understanding and engineering lignification in fibres.

show abstract

Section: Gene Expression Analysis In Qrt-pcrmentioning

confidence: 99%