Genomic and Allelic Analyses of Laccase Genes in Sugarcane (Saccharum spontaneum L.)

Laccases play crucial roles in catalyzing lignin and flavonoid biosynthesis in plants, and are predominantly involved in lignin breakdown of bacteria and fungi. Lignin distributes in all parts of plant and is a key component in plant morphogenesis. The complex sugarcane genome limited the study of laccase genes, but our completed reference genome of tetraploid S. spontaneum AP85-441 makes it possible to study this gene family. We identified 29 laccase genes, and 10 genes with 4 alleles, 9 genes with 3 alleles, 5 genes with 2 alleles, 5 genes with 1 allele in sugarcane. Among them 4 genes have tandemly dupicated paralogs; and 12 genes have dispersely distributed paralogs. They distributed unevenly among 27 of 32 chromosomes, and 9 (31.03%) genes located in Chromosome 3. Phylogeny and conserved domain suggested sugarcane laccase genes had the highest similarity with sorghum, and laccase10 was the most conserved gene in monocots and dicotyledons. We found sugarcane laccase genes were regulated by light signal, phytohormones, abiotic stress and some tissue-specific transcription factors by predicted cis-elements in the promoters. Nine laccase genes had miR397 and miR528 target sites, which have been reported as post-transcriptionally regulated laccase genes. Four laccase genes had 4 new miRNA target sites, including stem specific miRNA. Analysis of RNA-seq data of different developmental stages of leaves and stems showed that 27 genes had expression of those tissues, and most of them mainly express in stems. Among them laccase 4 and laccase10 showed the highest expression level in mature stems, while laccase27 showed the highest expression in seedling leaves. Our results show the potential function of sugarcane laccase genes in catalyzing lignin biosynthesis, stress resistance, and morphogenesis. These findings and genomic resources will facilitate research on improving stress tolerance, lignin content, and biomass yield in sugarcane.