Genome-wide analysis of the lignin toolbox formorusand the roles of lignin related genes in response to zinc stress

Abstract

Mulberry (Morus, Moraceae) is an important economic plant with nutritional, medicinal, and ecological values. Lignin in mulberry can affect the quality of forage and the saccharification efficiency of mulberry twigs. The availability of the Morus notabilis genome makes it possible to perform a systematic analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway, providing the core genes for the lignin toolbox in mulberry. We performed genome-wide screening, which was combined with de novo transcriptome data for Morus notabilis and Morus alba variety Fengchi, to identify putative members of the lignin gene families followed by phylogenetic and expression profile analyses. We focused on bona fide clade genes and their response to zinc stress were further distinguished based on expression profiles using RNA-seq and RT-qPCR. We finally identified 31 bona fide genes in Morus notabilis and 25 bona fide genes in Fengchi. The putative function of these bona fide genes was proposed, and a lignin toolbox that comprised 19 genes in mulberry was provided, which will be convenient for researchers to explore and modify the monolignol biosynthesis pathway in mulberry. We also observed changes in the expression of some of these lignin biosynthetic genes in response to stress caused by excess zinc in Fengchi and proposed that the enhanced lignin biosynthesis in lignified organs and inhibition of lignin biosynthesis in leaf is an important response to zinc stress in mulberry.

WITHDRAWN: Lignin metabolism involved in zinc-alleviating effects on iron-induced phytotoxicity in wheat roots

“…Liu et al (2015) observed that the up-regulation of PAL and 4CL gene expression in rice roots was responsible for the elevation of lignin content with increasing Cu concentration. In addition, high expression of 4CL and CAD genes was related to the ligni cation in morus under excess Zn stress (Chao et al 2021). The present data indicated that Fe-induced signi cant increases of PAL, 4CL and CAD activities (Fig.…”

The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis

“…Among them, CCR catalyzes the coumarin production, plays an important role in regulating the carbon flow of lignin biosynthesis pathway. In total, we found 31 CCR homology genes in lacquer genome, while 31 are present in pear ( Pyrus bretschneideri ) ( Cheng et al., 2017 ), 14 are present in soybean ( Cui et al., 2021 ), and six are present in mulberry ( Chao et al., 2021 ). The TvCCR phylogenetic tree constructed with CCRs from Arabidopsis thaliana , O. sativa , Populus , as well as P. vera and S. birrea revealed that CCRs are clustered into four groups ( Figure S12 ), which indicated that CCRs had structural and functional divergence.…”

Comprehensive analysis of the MYB transcription factor gene family in Morus alba

“…Our previous reported RAN-seq data (Accession number: PRJNA660559) was used to obtain the expression profiles of R2R3 and 3R - MaMYB s in roots, stems and leaves [ 31 ]. Expression profile of R2R3 and 3R-MaMYB s in different fruit development stages was obtained using RNA-seq data with accession number: CRA006074 in national genomics data center (NGDC).…”