Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Aug 6:9:e11964.
doi: 10.7717/peerj.11964. eCollection 2021.

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

Nan Chao  1   2 , Ting Yu  1 , Chong Hou  1 , Li Liu  1   2 , Lin Zhang  1   2
Affiliations

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

Nan Chao et al. PeerJ. .

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.

Keywords: Gene family; Genome-wide; Lignin; Mulberry; Zinc stress.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Phylogenetic analysis and expression profile of PAL and 4CL gene family in mulberry.
(A) Phylogenetic analysis of PALs; (B) Expression profiles of PAL gene family in different tissues or organs in Morus notabilis and Fengchi; (C) Phylogenetic analysis of 4CLs; (D) Expression profiles of 4CL gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating PALs or 4CLs from dicots, blue full circles indicating PALs or 4CLs from monocots, green full circles indicating PALs or 4CLs from gymnosperms and yellow full circles indicating PALs from ferns or moss. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without Zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment. Bona fide clades were marked using different color shading.
Figure 2
Figure 2. Phylogenetic analysis and expression profile of C3′H and C4H gene families in mulberry.
(A) Phylogenetic analysis of C4Hs; (B) Phylogenetic analysis of C3′Hs. (C) Expression profiles of C3′H and C4H gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating proteins from dicots, blue full circles indicating proteins from monocots, green full circles indicating proteins from gymnosperms and yellow full circles indicating proteins from ferns or moss. Bona fide clades were marked using different color shadings. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment.
Figure 3
Figure 3. Phylogenetic analysis and expression profile of HCT and CSE gene families in mulberry.
(A) Phylogenetic analysis of HCTs; (B) Phylogenetic analysis of CSEs; (C) Expression profiles of HCT and CSE gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating proteins from dicots, red empty circles indicating HQTs, blue full circles indicating proteins from monocots, green full circles indicating proteins from gymnosperms and yellow full circles indicating proteins from ferns or moss. Bona fide clades were marked using different color shadings. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment.
Figure 4
Figure 4. Phylogenetic analysis and expression profile of CCoAOMT and COMT gene families in mulberry.
(A) Phylogenetic analysis of CCoAOMTs; (B) Phylogenetic analysis of COMTs; (C) Expression profiles of CCoAOMT and COMT gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating proteins from dicots, blue full circles indicating proteins from monocots, green full circles indicating proteins from gymnosperms and yellow full circles indicating proteins from ferns or moss. Bona fide clades were marked using different color shadings. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment.
Figure 5
Figure 5. Phylogenetic analysis and expression profile of F5H gene family in mulberry.
(A) Phylogenetic analysis of F5Hs; (B) Expression profiles of F5H gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating F5Hs from dicots, blue full circles indicating F5Hs from monocots, green full circles indicating F5Hs from gymnosperms and yellow full circles indicating F5Hs from ferns or moss. Bona fide clades were marked using different color shadings. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment.
Figure 6
Figure 6. Phylogenetic analysis and expression profile of CCR and CAD gene families in mulberry.
(A) Phylogenetic analysis of CCRs; (B) Phylogenetic analysis of CADs; (C) Expression profiles of CCR and CAD gene family in different tissues or organs in Morus notabilis and Fengchi. Red full circles indicating proteins from dicots, blue full circles indicating proteins from monocots, green full circles indicating proteins from gymnosperms and yellow full circles indicating proteins from ferns or moss. Bona fide clades were marked using different color shadings. Putative protein sequences were used for phylogenetic analysis and the sequences information is available in Table S2. Mn indicating Morus notabilis and Fc indicating Fengchi. L0, leaf without zinc treatment; S0, stem without zinc treatment; R0, root without zinc treatment.
Figure 7
Figure 7. Expression change of bona fide clade genes in response to excess zinc stress in mulberry.
(A) Fold change of expression levels of 23 bona fide genes in Fengchi after excess zinc treatment; (B) Overall change of monolignol pathway in different organs after excess zinc treatment in Fengchi; (C) Clustering of 23 bona fide clade genes expression pattern in response to Zinc stress. Two biological replicates with three technical replicates respectively were performed for qRT-PCR. P-value was calculated using SPSS 19.0. An asterisk (*) indicates 0.01 < p <0.05; two asterisks (**) indicates 0.001 < p < 0.01 and three asterisks (***) indicates p < 0.001.
See this image and copyright information in PMC

References

    1. Abdulrazzak N, Pollet B, Ehlting J, Larsen K, Asnaghi C, Ronseau S, Proux C, Erhardt M, Seltzer V, Renou JP, Ullmann P, Pauly M, Lapierre C, Werck-Reichhart D. A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth. Plant Physiology. 2006;140(1):30–48. doi: 10.1104/pp.105.069690. - DOI - PMC - PubMed
    1. Bhardwaj R, Handa N, Sharma R, Kaur H, Kohli S, Kumar V, Kaur P. Lignins and abiotic stress: an overview. In: Ahmad P, Wani M, editors. Physiological Mechanisms and Adaptation Strategies in Plants Under Changing Environment. New York: Springer; 2014. pp. 267–296.
    1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: Architecture and applications. BMC Bioinformatics. 2009;10(1):421. doi: 10.1186/1471-2105-10-421. - DOI - PMC - PubMed
    1. Carocha V, Soler M, Hefer C, Cassan-Wang H, Fevereiro P, Myburg AA, Paiva JA, Grima-Pettenati J. Genome-wide analysis of the lignin toolbox of Eucalyptus grandis. New Phytologist. 2015;206(4):1297–1313. doi: 10.1111/nph.13313. - DOI - PubMed
    1. Chao N, Jiang WT, Wang XC, Jiang XN, Gai Y. Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants. Tree Physiology. 2019;39(12):2019–2026. doi: 10.1093/treephys/tpz098. - DOI - PubMed

LinkOut - more resources