Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

Abstract

For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

“…In addition, the synteny relationship between N. nucifera and N. colorata and between N. nucifera and C. kanehirae is 2:2 and 2:4, respectively (Additional file 1: C. kanehirae. Several earlier studies showed that the WGD in N. nucifera is lineagespecific rather than eudicot-wide, rejecting the possibility that any WGD occurred in the common ancestor of all extant eudicots [13,43,44]. The collinear relationships between T. sinense/T.…”

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

“…The ratio of filtered high-quality reads mapped to the miRBase is 0.33%, i.e. a total of 50,866 reads aligned to the reference genome (nelumbo.biocloud.net) ( Table 1) [29]. After merging with previous lotus miRNAs [27] and removing the redundant (overlapping) hairpin loci, a total of 1103 potential mature miRNA and 104 miRNA-star (the opposite strand of miRNA from dsRNA) sequences were identified, and these miRNAs are produced by 1416 pre-miRNAs (hairpin loci) ( Fig.…”

“…Before miRNA identification, the retained reads were further processed using the miRDeep2 [56]. After quality filtering, the Bowtie was used to map the high-quality reads to the reference genome (nelumbo.biocloud.net) with zero mismatches [29,57]. The mapped small RNAs were guided by the known precursor miRNA dataset (miRbase 22.0) to identify potential miRNA precursors in the lotus genome, allowing the duplicate (hairpin) loci less than five.…”

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

“…The ratio of ltered high-quality reads mapped to the miRBase is 0.33%, i.e. a total of 50 866 reads aligned to the reference genome (nelumbo.biocloud.net) ( Table 1) [29]. After merging with previous lotus miRNAs [27] and removing the redundant (overlapping) hairpin loci, a total of 1103 potential mature miRNA and 104 miRNA-star sequences were identi ed, and these miRNAs are produced by 1416 pre-miRNAs (hairpin loci) ( Fig.…”

“…After quality ltering, the Bowtie was used to map the high-quality reads to the reference genome (nelumbo.biocloud.net) with zero mismatches [29,56]. The mapped small RNAs were guided by the known precursor miRNA dataset (miRbase 22.0) to identify potential miRNA precursors in the lotus genome, allowing the duplicate (hairpin) loci less than ve.…”