Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)

Abstract

The evolutionary dynamics and tissue specificity of protein-coding genes are well documented in plants. However, the evolutionary consequences of small RNAs (sRNAs) on tissue-specific functions remain poorly understood. Here, we performed integrated analysis of 195 deeply sequenced sRNA libraries of maize B73, representing more than 10 tissues, and identified a comprehensive list of 419 maize microRNA (miRNA) genes, 271 of which were newly discovered in this study. We further characterized the evolutionary dynamics and tissue specificity of miRNA genes and corresponding miRNA isoforms (isomiRs). Our analysis revealed that tissue specificity of isomiR events tends to be associated with miRNA gene abundance and suggested that the frequencies of isomiR types are affected by the local genomic regions. Moreover, genome duplication (GD) events have dramatic effect on evolutionary dynamics of maize miRNA genes, and the abundance divergence for tissue-specific miRNA genes is associated with GD events. Further study indicated that duplicate miRNA genes with tissue-specific expression patterns, such as miR2275a, a phased siRNA (phasiRNA) trigger, contribute to phenotypic traits in maize. Additionally, our study revealed the expression preference of 21- and 24-nt phasiRNAs in relation to tissue specificity. This large-scale sRNAomic study depicted evolutionary implications of tissue-specific maize sRNAs, which coordinate genome duplication, isomiR modification, phenotypic traits and phasiRNAs differentiation.

Keywords: genome duplication; maize; microRNA; phasiRNAs; tissue specificity.

Figure 1

Bioinformatics pipeline for the identification of miRNA genes in maize.

Figure 2

Genome-wide characteristics of maize miRNA genes. (A) Chromosomal distribution of 419 maize miRNA genes. Newly identified miRNA genes were labeled as red. The black filled circles represent centromeres (B) Statistics of different isomiR types in the maize genome.

Figure 3

Overview of tissue-specific patterns of maize miRNA genes.

Figure 4

Dynamic patterns of isomiR events in terms of tissue types and genomic environments. (A) Abundance of isomiRs varied widely among individual tissues. (B) Correlation between the abundance of isomiR events and PCG-harbored miRNA genes in all tissue samples. (C) Correlation between the abundance of isomiR events and TE-harbored miRNA genes in all tissue samples. (D) Correlation between the abundance of isomiR events and UI-harbored miRNA genes in all tissue samples. (E) Comparisons of isomiR abundance among seven isomiR types in PCG-harbored miRNA genes. (F) Comparisons of isomiR abundance among seven isomiR types in TE-harbored miRNA genes. (G) Comparisons of isomiR abundance among seven isomiR types in UI-harbored miRNA genes. Statistically significant differences in (E, F and G) were determined using Student's t-test and **indicated P-value < 0.05.

Figure 5

Evolutionary consequence of the miR2275 family in maize. (A) GWAS results, which overlapped with miR2275 loci. The gray horizontal dashed lines indicate the significance threshold of GWAS (1 × 10⁻⁵). The mature miRNA sequences are highlighted in red and the miRNA star sequences are highlighted in yellow. Black arrows indicate significant mutation sites. Days to anthesis (DTA) and days to silk production (DTS) are labeled in red and green, respectively. (B) Duplication status of miR2275 family members. Green boxes indicate PCGs, red boxes represent miR2275 gene family members, and the blue box represents helitron transposon. (C) Comparison of mature miRNA accumulation between 5′ and 3′ arms in individual miR2275 members. (D) Accumulation levels of seven miR2275 genes in individual tissue samples. The accumulation levels were calculated as sum of miRNA mature sequences, miRNA star sequences and isomiRs.

Figure 6

Differentiation of 21- and 24-nt PHAS loci in relation to tissue specificity. (A) Heat maps depicted the abundance of 21-nt PHAS loci (left) and 24-nt PHAS loci (right) in individual tissue samples. Solid bubbles represent the total abundance of phasiRNAs and corresponding miRNA triggers. Circles represent the number of PHAS loci. In the heatmaps, PHAS loci were clustered according to the miRNA triggers. Color bars on the top of heatmaps represent different triggers, among which orange represents miR2118 and red represents miR2275. (B) Heat maps depicted the abundance of 21- and 24-nt PHAS loci in four categories (PCG harbored, TE harbored, duplicates, and singletons). The dashed boxes indicated the divergence between the abundance of 21- and 24-nt PHAS loci in corresponding tissue samples.