Heterogeneous evolution of Ty3-gypsy retroelements among bamboo species.

Ty3-gypsy long-terminal repeat retroelements are ubiquitously found in many plant genomes. This study reports the occurrence of heterogeneous Ty3-gypsy retroelements in four representative bamboo species: Phyllostachys heterocycla (Carr.) Mitford cv. pubescens, P. heterocycla (Carr.) Mitford cv. heterocycla, Dendrocalamopsis oldhami, and Pleioblastus fortunei. Using degenerate oligonucleotide primers corresponding to the conserved domains of reverse transcriptase (rt) genes of Ty3-gypsy retroelements, 165 distinct sequences were amplified from genomic DNA. The length of the nucleotide sequences varied from 366 to 438 bp. The sequences demonstrated a high heterogeneity, with homology ranging from 52.2 to 99.8%. A phylogenetic tree was constructed, including Arabidopsis thaliana and Oryza sativa. Bamboo Ty3-gypsy sequences formed three distinct retroelement clusters (gypsy I-III). Further analysis indicated that there were not only nearly identical Ty3-gypsy retroelements found in distantly related species, but also highly diverse Ty3-gypsy retroelements observed in closely related species. The results of this study provide genetic and evolutionary information about the bamboo genome that could contribute to further studies of repetitive elements in bamboo as well as in other species.

Identification of genes involved in spontaneous leaf color variation in Pseudosasa japonica.

Spontaneous leaf color variation in bamboo provides the opportunity to study the mechanisms of leaf color formation and the breeding of ornamental bamboos. Despite the fact that many genes are known to be involved in leaf color variation in model plants, molecular mechanisms governing natural leaf color variation in bamboo have remained obscure. This study aimed to identify the genes responsible for the occurrence of such phenomena in bamboo using the suppression subtractive hybridization (SSH) method between green and albino leaves in Pseudosasa japonica f. A total of 1062 and 1004 differentially expressed transcripts were obtained from the forward and reverse SSH libraries, respectively. Subsequently, 59 differentially expressed unigenes with potential roles in leaf color formation, predicted via computational analysis of their functional relevance, were selected for further analysis using qPCR. Ten genes, involved in photosynthesis, plastid development, and cation signal transduction, showed 2-fold changes in expression levels between green and albino leaves. Further expression pattern analyses of these genes at three developmental stages revealed much lower expression abundance of Lhca1-encoded chlorophyll a/b binding protein in the albino leaves than in the green leaves. Our results suggest that, together with the concatenated negative pressure for subsequent photosynthetic processes, the albino phenotype is at least partly attributable to chloroplast inner membrane damage or to the impairment of photosynthetic pigment accumulation, which results from low Lhca1 expression.

PpPIF-1: first isolated full-length PIF-like element from the bamboo Phyllostachys pubescens.

PIF-like elements are the first-described members of a recently discovered and widespread superfamily of DNA transposons, named PIF/Harbinger. Complete and partial PIF-like elements have been isolated from hundreds of plant species. Previously, we identified 139 partial PIF-like transposases in the Bambusoideae, of which three were from the bamboo species Phyllostachys pubescens. Here we report identification and isolation of the first full-length PIF-like element (PpPIF-1) from P. pubescens; identification was made by chromosome walking, based on a modified magnetic enrichment procedure that allows efficient cloning of flanking sequences up to 3 kb in length. PpPIF-1 is 5953 bp in length, with 20-bp imperfect inverted terminal repeats and 3-bp target site duplications. This element contains two open reading frames, one encoding a putative transposase, including the complete DDE-domain typical of PIF/Harbinger elements from plants, and the other encoding a DNA-binding protein. There are seven termination codons and two frameshift mutations in the open reading frames, probably due to vertical inactivation.

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats.

Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FL-cDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.