Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

Abstract

Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%-25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.

Figure 1.

Comparative analysis between wheat chromosome 3A and the sequenced genomes of B. distachyon, rice, and sorghum. A, Comparison of the wheat chromosome 3A SGO map (Ta3A) with sorghum chromosomes 3 and 9 (Sb3 and Sb9), rice chromosomes 1 and 5 (Os1 and Os5), and B. distachyon chromosome 2 (Bd2). Ancestral chromosome duplications predating the divergence of wheat, rice, B. distachyon, and sorghum are colored in blue; chromosomal bins enriched for BLASTN hits with chromosome 3A contigs are colored in orange. B, Location of the wheat chromosome 3A centromere was inferred by BLASTN comparison of SGO with the 454 reads generated for flow-sorted 3AS and 3AL chromosomal arms. The locations of two chromosome 3A contigs on the SGO map (SGO1221 and SGO1367) showing similarity to previously mapped EST markers flanking the wheat centromere are shown.

Figure 2.

Proportion of alternative and conserved coding segments between wheat and the model genomes. A, Classification of coding segments used for comparison of gene exon-intron structure among wheat, rice, and B. distachyon. Only the wheat-rice comparison is shown. The protein isoforms of rice or B. distachyon were aligned to orthologous gene models in wheat. Differences in exon-intron structure in these pairwise comparisons were referred to as coding segments. Thus, each exon in our analysis was represented by a combination of several coding segments. Coding segments that were present in both compared orthologs were referred to as constitutive coding segments; coding segments that were present in only one of the two compared orthologs were referred to as alternative coding segments. The following categories of minievents resulting in gene structure changes were recorded: conserved exons (CE), acquired exons (AE), and lost exons (LE). Both AE and LE correspond to alternative coding segments; CE corresponds to a subset of constitutive coding segments. B, The proportion of AE, LE, and CE between the compared genes, relative to the total number of coding segments, was used to assess the level of gene structure conservation among orthologous genes of wheat (W), B. distachyon (B), and rice (R). Gene structure evolution was compared between wheat chromosome 3A and model genomes (3A versus R, 3A versus B), between two model grass genomes (B versus R), between a set of wheat genes located on other chromosomes (non-3A) and model genomes (W versus R, W versus B), and between homeologous genes on wheat chromosomes 3A, 3B, and 3D (3A versus 3B, 3A versus 3D).

Figure 3.

Evolution of coding sequences in the wheat genome. A, Distribution of pairwise estimates of d_N/d_S in a set of orthologous genes from wheat (W), B. distachyon (B), and rice (R). B, H₀ and H_A are null (codon mutation rates in the wheat and B. distachyon lineages are equal; v1 = v2) and alternative (codon mutation rates in the wheat and B. distachyon lineages are different; v1 ≠ v2) hypotheses, respectively; v1 and v2 are expected codon mutation rates in wheat and B. distachyon, respectively. C, Log₂ ratio of codon mutation rates in the wheat (v1) and B. distachyon (v2) lineages estimated for an orthologous set of 986 genes (Supplemental Table S19). The significance threshold (P ≤ 0.05) is shown by the red dashed line. D, Distribution of d_N/d_S estimates, PTCs (blue bars), and LE/AE events (red bars) along wheat chromosome 3A. The 95th percentile of d_N/d_S ratio distribution in a window of five genes (dashed lines) was calculated by permutation (see “Materials and Methods”).