The evolution of plant microRNAs: insights from a basal eudicot sacred lotus.

microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus. Further analyses of lotus genome revealed that there is an association between loss of miRNA families in descendent plants and in duplicated genomes. Gene dosage balance is crucial in maintaining those preferentially retained MIRNA duplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putative MIRNA-likes. Additionally, the MIRNAs participating in lotus pollen-pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence in MIRNAs escalates expression divergence of their target genes between temperate and tropical lotus during rhizome and leaf growth. Overall, our study unravels several important factors and selection that determine the miRNA family distribution in plants and duplicated genomes, and provides evidence for functional impact of MIRNA sequence evolution.

Shi T ，Wang K ，Yang P 《-》

Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera.

Hu J ，Jin J ，Qian Q ，Huang K ，Ding Y ... -  《-》

Practical halving; the Nelumbo nucifera evidence on early eudicot evolution.

We present a stepwise optimal genome halving algorithm designed for large eukaryote genomes with largely single-copy genes, taking advantage of a signature pattern of paralog distribution in ancient polyploids. This is applied to the genome of Nelumbo nucifera, the sacred lotus, which is the descendant of a duplicated basal eudicot genome. In concert with the reconstructed ancestor of the grape, we investigate early events in eudicot evolution and show that the chromosome number of the common ancestor of lotus and grape was likely between 5 and 7. We show that the duplication of the ancestor of lotus and the triplication of the ancestor of grape were not closely preceded by any additional such event before the divergence of their two lineages.

Zheng C ，Sankoff D 《-》

The sacred lotus genome provides insights into the evolution of flowering plants.

Sacred lotus (Nelumbo nucifera) is an ornamental plant that is also used for food and medicine. This basal eudicot species is especially important from an evolutionary perspective, as it occupies a critical phylogenetic position in flowering plants. Here we report the draft genome of a wild strain of sacred lotus. The assembled genome is 792 Mb, which is approximately 85-90% of genome size estimates. We annotated 392 Mb of repeat sequences and 36,385 protein-coding genes within the genome. Using these sequence data, we constructed a phylogenetic tree and confirmed the basal location of sacred lotus within eudicots. Importantly, we found evidence for a relatively recent whole-genome duplication event; any indication of the ancient paleo-hexaploid event was, however, absent. Genomic analysis revealed evidence of positive selection within 28 embryo-defective genes and one annexin gene that may be related to the long-term viability of sacred lotus seed. We also identified a significant expansion of starch synthase genes, which probably elevated starch levels within the rhizome of sacred lotus. Sequencing this strain of sacred lotus thus provided important insights into the evolution of flowering plant and revealed genetic mechanisms that influence seed dormancy and starch synthesis.

Wang Y ，Fan G ，Liu Y ，Sun F ，Shi C ，Liu X ，Peng J ，Chen W ，Huang X ，Cheng S ，Liu Y ，Liang X ，Zhu H ，Bian C ，Zhong L ，Lv T ，Dong H ，Liu W ，Zhong X ，Chen J ，Quan Z ，Wang Z ，Tan B ，Lin C ，Mu F ，Xu X ，Ding Y ，Guo AY ，Wang J ，Ke W ... -  《-》

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera).

Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.

Huang L ，Yang M ，Li L ，Li H ，Yang D ，Shi T ，Yang P ... -  《-》