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Uneven selection pressure accelerating divergence of Populus and Salix.

ABSTRACT: Populus (poplars) and Salix (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, Salix species are supposed to evolve faster than Populus species, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that Populus species may inherit the more incipient sex chromosome from their progenitor. Taken together, Salix is supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages.

SUBMITTER: Hou J

PROVIDER: S-EPMC6450953 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMicroRNAs (miRNAs) are small RNAs (sRNA) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in Arabidopsis and rice and partially investigated in other non-model plant species. To date, 109 and 62 miRNA families have been identified in Arabidopsis and rice respectively. However, only 33 miRNAs have been identified from the genome of the model tree species (Populus trichocarpa), of which 11 are Populus specific. The low number of miRNA families previously identified in Populus, compared with the number of families identified in Arabidopsis and rice, suggests that many miRNAs still remain to be discovered in Populus. In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing.ResultsAnalysis of almost eighty thousand small RNA reads allowed us to identify 123 new sequences belonging to previously identified miRNA families as well as 48 new miRNA families that could be Populus-specific. Comparison of the organization of miRNA families in Populus, Arabidopsis and rice showed that miRNA family sizes were generally expanded in Populus. The putative targets of non-conserved miRNA include both previously identified targets as well as several new putative target genes involved in development, resistance to stress, and other cellular processes. Moreover, almost half of the genes predicted to be targeted by non-conserved miRNAs appear to be Populus-specific. Comparative analyses showed that genes targeted by conserved and non-conserved miRNAs are biased mainly towards development, electron transport and signal transduction processes. Similar results were found for non-conserved miRNAs from Arabidopsis.ConclusionOur results suggest that while there is a conserved set of miRNAs among plant species, a large fraction of miRNAs vary among species. The non-conserved miRNAs may regulate cellular, physiological or developmental processes specific to the taxa that produce them, as appears likely to be the case for those miRNAs that have only been observed in Populus. Non-conserved and conserved miRNAs seem to target genes with similar biological functions indicating that similar selection pressures are acting on both types of miRNAs. The expansion in the number of most conserved miRNAs in Populus relative to Arabidopsis, may be linked to the recent genome duplication in Populus, the slow evolution of the Populus genome, or to differences in the selection pressure on duplicated miRNAs in these species.

Project description:BackgroundSalix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.ResultsWe constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).ConclusionsThe relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.

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Uneven selection pressure accelerating divergence of Populus and Salix.

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