Molecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley

Abstract

In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that HvHMTs and HvHDMs were highly expressed in specific tissues and had complex expression patterns under multiple stress treatments. In summary, the amplification and variation of HMT and HDM facilitate plant adaptation to complex terrestrial environments, while they are highly conserved in barley and play an important role in barley growth and development with abiotic stresses. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant HvHMTs and HvHDMs, and lay a foundation for further investigation of their functions in barley.

Keywords: HDM; HMT; barley; evolution; genome-wide analysis; histone methylation.

Figure 1

(a) Predicted number of HMT and HDM in different plant and algal species. Coloured squares indicate the protein predicted number from 0 (white) to 240 (red). (b) Similarity heatmap of HMT and HDM proteins in plant and algal species. Coloured squares indicate protein sequence similarity from zero (blue) to 100% (yellow). Gray squares indicate no proteins that satisfied the selection criteria.

Figure 2

Sequence homology of homologous genes among different germplasms. Coloured squares indicate protein sequence similarity from zero (blue) to 100% (red). Gray squares indicate no proteins that satisfied the selection criteria.

Figure 3

Phylogenetic and conserved domain analysis of SDG.

Figure 4

Analysis of promoter cis-acting elements of HvHMTs and HvHDMs. Gray squares indicates that the number of cis-acting elements in the gene is zero.

Figure 5

The spatiotemporal expression profile of HvHMTs and HvHDMs in different tissues or stages of barley. CAR15: bracts removed grains at 15 DPA; CAR5: bracts removed grains at 5 DPA; EPI: epidermis at 4 weeks old; ETI: etiolated from 10-day-old seedling; INF1: young inflorescences at 5 mm; INF2: young inflorescences at 1–1.5 cm; LEA: shoot at 10 cm from the seedlings; LEM: lemma at 6 weeks after anthesis; LOD: lodicule at 6 weeks after anthesis; NOD: developing tillers at six-leaf stage; RAC: rachis at 5 weeks after anthesis; ROO2: root from 4-week-old seedlings; ROO1: roots from the seedlings at 10 cm shoot stage; SEN: senescing leaf.

Figure 6

(a) RNA-seq: Cold, the expression patterns of HvHMTs and HvHDMs at 1 °C, −4 °C, and −8 °C. Drought, the expression patterns of HvHMTs and HvHDMs in sensitive varieties (Drought 1) and drought-tolerant varieties (Drought 2) under drought stress. Salt, the expression patterns of HvHMTs and HvHDMs in salt-sensitive varieties (Salt 1) and salt-tolerant varieties (Salt 2) under salt treatment for 4 h and 16 h. Waterlogging, the expression patterns of HvHMTs and HvHDMs of waterlogging tolerant varieties (Waterlogging 1) and medium waterlogging tolerant varieties (Waterlogging 2) under flooding. (b) RT-PCR: Expression of barley at 0, 3, 6, 12, and 24 h under low temperature, drought, salt, and flooding stress, and the expression of sensitive varieties (9127) and tolerant varieties (9117) under 50 Gy and 200 Gy intensity of gamma ray irradiation. Error bars represent ± SD from three biological repeats. Lowercase letters above bars indicate a significant difference (p < 0.05, LSD) among the treatments.