Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize

• Main Authors: Weina Si, Tianlu Hang, Mingyue Guo, Zhen Chen, Qizhi Liang, Longjiang Gu, Ting Ding
• Format: Article
• Language: English
• Published: MDPI AG 2019-11-01
• Series: International Journal of Molecular Sciences
• Subjects: <i>tlc</i> genes; gene duplication; subfunctionalization; maize
• Online Access: https://www.mdpi.com/1422-0067/20/21/5484

TLC (TRAM/LAG/CRN8) proteins play important roles in ceramide metabolism and mycotoxin resistance. Herein a comparative genomics analysis of TLCs was performed in 31 plant and 3 species from other kingdoms, with an emphasis mainly on maize. TLCs were conserved across kingdoms and expanded in angiosperms, largely due to whole-genome/segmental duplication (WGD/SD) under purifying selection. Phylogeny reconstruction by maximum-likelihood method uncovered five TLC clades, subsequently named as TRAM/LAG, CLN8, PS-TLC, TM136 and TLCD clades. Each clade of TLCs shared specific transmembrane regions and motif composition. Divisions of conserved motifs to subunits may have occurred in TM136-type TLCs. Focusing on maize, five WGD and two DNA-mediated transposed duplication (TD) pairs were discovered, accounting for 61.11% <i>ZmTLCs</i>. Combined with further expression analysis, significant divergence was found in expression patterns between most maize WGD pairs, indicating subfunctionalization or/and neofunctionalization. Moreover, <i>ZmTLC5</i>, a deduced parental copy in a TD pair, was highly induced under FB₁ and fungus pathogen injection and exhibited potential capacity to respond to environmental stimuli. Additionally, population genetics analysis showed that <i>ZmTLC10</i> in the CLN8-clade may have experienced significant positive selection and differentiated between wild and inbred maize populations. Overall, our results help to decipher the evolutionary history of <i>TLCs</i> in maize and plants, facilitating further functional analysis of them.