Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

A Geranylfarnesyl Diphosphate Synthase Provides the Precursor for Sesterterpenoid (C25) Formation in the Glandular Trichomes of the Mint Species Leucosceptrum canum.

Plant sesterterpenoids, an important class of terpenoids, are widely distributed in various plants, including food crops. However, little is known about their biosynthesis. Here, we cloned and functionally characterized a plant geranylfarnesyl diphosphate synthase (Lc-GFDPS), the enzyme producing the C25 prenyl diphosphate precursor to all sesterterpenoids, from the glandular trichomes of the woody plant Leucosceptrum canum. GFDPS catalyzed the formation of GFDP after expression in Escherichia coli. Overexpressing GFDPS in Arabidopsis thaliana also gave an extract catalyzing GFDP formation. GFDPS was strongly expressed in glandular trichomes, and its transcript profile was completely in accordance with the sesterterpenoid accumulation pattern. GFDPS is localized to the plastids, and inhibitor studies indicated its use of isoprenyl diphosphate substrates supplied by the 2-C-methyl-D-erythritol 4-phosphate pathway. Application of a jasmonate defense hormone induced GFDPS transcript and sesterterpenoid accumulation, while reducing feeding and growth of the generalist insect Spodoptera exigua, suggesting that these C25 terpenoids play a defensive role. Phylogenetic analysis suggested that GFDPS probably evolved from plant geranylgeranyl diphosphate synthase under the influence of positive selection. The isolation of GFDPS provides a model for investigating sesterterpenoid formation in other species and a tool for manipulating the formation of this group in plants and other organisms.

Triosephosphate isomerase genes in two trophic modes of euglenoids (euglenophyceae) and their phylogenetic analysis.

Two different length cDNAs encoding triosephosphate isomerase (TIM) were identified in the two trophic modes of euglenoids, the phototrophic Euglena gracilis and Euglena intermedia and the saprotrophic Astasia longa. Sequence analyses and presequence prediction indicated that the shorter cDNA encodes a cytosolic TIM and the longer cDNA encodes a plastid TIM (pTIM). The typical presequence of the putative A. longa pTIM and the high sequence similarity between A. longa pTIM and E. gracilis pTIM imply that A. longa pTIM is targeted to plastids. Therefore, although the plastids of A. longa have lost the ability of photosynthesis, they might retain other TIM-related function(s), such as glycolysis and the synthesis of isopentenyl diphosphate or fatty acids. Including the TIM sequences obtained by us from chlorophytes and rhodophytes, our phylogenetic analyses indicated that euglenoid TIMs group neither with TIMs of kinetoplastids, which share the nearest common ancestor with euglenoids, nor are closely related to TIMs of chlorophytes, which are considered to be the donors of euglenoid plastids through secondary endosymbiosis. Instead, they group with TIMs of rhodophytes. In addition, our amino acid sequence alignment and structure modeling showed that TIMs of euglenoids and rhodophytes share a unique 2-aa insertion within their loop-4 areas. Therefore, either tim convergent evolution or lateral gene transfer (more probably) might have occurred between euglenoids and rhodophytes after the divergence of euglenoids with kinetoplastids.