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Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification

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Abstract

Main conclusion

Five laccase genes are potentially involved in developmental lignification in the model C4 grass Setaria viridis and their different tissue specificities suggest subfunctionalization events.

Abstract

Plant laccases are copper-containing glycoproteins involved in monolignol oxidation and, therefore, their activity is essential for lignin polymerization. Although these enzymes belong to large multigene families with highly redundant members, not all of them are thought to be involved in lignin metabolism. Here, we report on the genome-wide characterization of the laccase gene family in the model C4 grass Setaria viridis and further identification of the members potentially involved in monolignol oxidation. A total of 52 genes encoding laccases (SvLAC1 to SvLAC52) were found in the genome of S. viridis, and phylogenetic analyses showed that these genes were heterogeneously distributed among the characteristic six subclades of the family and are under relaxed selective constraints. The observed expansion in the total number of genes in this species was mainly caused by tandem duplications within subclade V, which accounts for 68% of the whole family. Comparative phylogenetic analyses showed that the expansion of subclade V is specifically observed for the Paniceae tribe within the Panicoideae subfamily in grasses. Five SvLAC genes (SvLAC9, SvLAC13, SvLAC15, SvLAC50, and SvLAC52) fulfilled the criteria established to identify lignin-related candidates: (1) phylogenetic proximity to previously characterized lignin-related laccases from other species, (2) similar expression pattern to that observed for lignin biosynthetic genes in the S. viridis elongating internode, and (3) high expression in S. viridis tissues undergoing active lignification. In addition, in situ hybridization experiments not only confirmed that these selected SvLAC genes were expressed in lignifying cells, but also that their expression showed different tissue specificities, suggesting subfunctionalization events within the family. These five laccase genes are strong candidates to be involved in lignin polymerization in S. viridis and might be good targets for lignin bioengineering strategies.

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Abbreviations

SCW:

Secondary cell wall

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Acknowledgements

This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) via the BIOEN Young Investigators Awards research grant (Processo FAPESP no. 2015/02527-1). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—Finance Code 001. IC thanks FAPESP for the SPRINT Project Grant number 2016/50189-0. IC is indebted to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the research fellowship 302927/2018-2. MSS was funded by CAPES for a predoctoral fellowship. GGC was funded by CNPq-PIBIC for a scientific initiation fellowship. SSF was funded by FAPESP for a postdoctoral fellowship (Processo FAPESP no. 2016/06917-1).

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Correspondence to Igor Cesarino.

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Electronic supplementary material

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Peptide sequences of all 52 laccases of S. viridis in FASTA format (TXT 31 kb)

Dataset of laccase peptide sequences from Arabidopsis thaliana + grasses in FASTA format (TXT 319 kb)

Dataset of laccase peptide sequences from Arabidopsis thaliana + eudicots in FASTA format (TXT 157 kb)

Dataset of laccase peptide sequences from Arabidopsis thaliana + other monocots + Amborella trichopoda in FASTA format (TXT 54 kb)

Exon-intron structure and conserved domains distribution of SvLAC genes/proteins (PDF 357 kb)

Maximum likelihood tree built with laccase proteins from Arabidopsis thaliana and grasses. Numbers at nodes indicate branch support performed by the SH-aLRT test and the ultrafast bootstrap test, respectively (PDF 89 kb)

Maximum likelihood tree built with laccase proteins from Arabidopsis thaliana and eudicots. Numbers at nodes indicate branch support performed by the SH-aLRT test and the ultrafast bootstrap test, respectively (PDF 45 kb)

Maximum likelihood tree built with laccase proteins from Arabidopsis thaliana and other monocots + Amborella trichopoda. Numbers at nodes indicate branch support performed by the SH-aLRT test and the ultrafast bootstrap test, respectively (PDF 29 kb)

List of primers used in this study (XLSX 21 kb)

In silico prediction of some physico-chemical properties of SvLAC proteins (XLSX 14 kb)

RNAseq expression data (FPKM) of all laccase genes in S. viridis retrieved from the work of Martin et al. 2016. Data for different subclades are shown in different sheets (XLSX 42 kb)

Analysis of the presence of stress-related cis-elements in the promoter of SvLAC genes (XLSX 21 kb)

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Simões, M.S., Carvalho, G.G., Ferreira, S.S. et al. Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification. Planta 251, 46 (2020) doi:10.1007/s00425-020-03337-x

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Keywords

  • Gene expression
  • Grasses
  • In situ hybridization
  • Laccases
  • Lignin
  • Monolignol polymerization
  • Paniceae