Multiple variation patterns of terpene synthases in 26 maize genomes

Abstract

Terpenoids are important compounds associated with the pest and herbivore resistance mechanisms of plants; consequently, it is essential to identify and explore terpene synthase (TPS) genes in maize. In the present study, we identified 31 TPS genes based on a pan-genome of 26 high-quality maize genomes containing 20 core genes (present in all 26 lines), seven dispensable genes (present in 2 to 23 lines), three near-core genes (present in 24 to 25 lines), and one private gene (present in only 1 line). Evaluation of ka/ks values of TPS in 26 varieties revealed that TPS25 was subjected to positive selection in some varieties. Six ZmTPS had ka/ks values less than 1, indicating that they were subjected to purifying selection. In 26 genomes, significant differences were observed in ZmTPS25 expression between genes affected by structural variation (SV) and those not affected by SV. In some varieties, SV altered the conserved structural domains resulting in a considerable number of atypical genes. The analysis of RNA-seq data of maize Ostrinia furnacalis feeding revealed 10 differentially expressed ZmTPS, 9 of which were core genes. However, many atypical genes for these responsive genes were identified in several genomes. These findings provide a novel resource for functional studies of ZmTPS.

The terpene synthase gene family in maize – a clarification of existing community nomenclature

“…Please note that this table also includes obvious pseudogenes, because it has been shown that a pseudogene in one maize line can be functional in another line [3,5,6] KS(L3)/D5 to highlight its activity as an ent-kaurene synthase. Note that this nomenclature includes not only the 43 TPS gene loci found in the B73 reference genomes GRAMENE 4.0 and NAM 5.0 (www.maizegdb.org), but also four additional TPS genes not present in B73 but identified in other maize lines by Sun and coworkers [7].…”

“…The amazing quantitative and qualitative plasticity of the maize TPS gene family was confirmed in a recent paper by Sun and coworkers, who analyzed TPS genes in the genomes of 26 inbred lines [7]. However, only 31 gene loci were included in this analysis, resulting in one-third of the already characterized TPS genes being omitted by the authors.…”