Diversity and evolution of Ty1-copia retroelements in representative tribes of Bambusoideae subfamily

Abstract

Ty1-copia retroelements have been found in all major plants and are largely responsible for the huge differences in the genome size. In this study we isolated and sequenced Ty1-copia reverse transcriptase (rt) gene fragments from 44 representative species of bamboo and nine cultivars or forms of Phyllostachys pubescens. Phylogenetic analysis of 72 distinct Ty1-copia rt sequences showed that Ty1-copia retroelements were widespread, diverse and abundant in these species of Bambusoideae subfamily. In addition, a molecular phylogeny of the species of the Bambusoideae subfamily was established by using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) sequences. The comparison between ITS- and Ty1-copia rt- based trees is obviously incongruent. The results suggested either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral Ty1-copia retroelement polymorphism followed by different evolution and stochastic losses.

Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens

“…P. pubescens has 2n = 48 chromosomes and is thought to be tetraploid (Li et al 1999). The genome is >2000 Mb, which is approximately 5.4 times larger than diploid cultivated rice (Gui et al 2007), and it contains a large number of TEs (Zhong et al 2010; Zhou et al 2010a, [b], [c]). The slightly higher attrition rate we encountered therefore seems reasonable when considering the chromosomal polyploidy, size and TE content of the genome .…”

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

“…We previously reported a phylogenic analysis of the partial polypeptide sequences of 29 reverse transcriptase (approximately 90 amino acids) from Ty1-copia elements in P. pubescens and nine diverse cultivars, revealing that the elements were both diverse and abundant in the P. pubescens genome (Zhou et al, 2010c). Here we extended the analysis of the fullreverse transcriptase sequences from 24 Ty1-copia and 31 Ty3-gypsy elements from P. pubescens and 36 related elements from other Poaceae species (rice, maize and sorghum).…”

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

“…Particularly, Ty3‐gypsy and Ty1‐copia are found to have the highest copy numbers (Peng, Lu, et al, 2013; Zhao, Gao, et al, 2018). Given that LTR retrotransposons play significant roles in bamboo genome evolution (Li, Ramakrishnan, et al, 2020), Ty3‐gypsy and Ty1‐copia elements are thought to be responsible for enlarging the genome size of moso bamboo (Zhou, Hu, & Zhu, 2017; Zhou, Zhong, Zhang, Tang, & Tang, 2010). Moreover, the LTRs produce more than 30% of small interfering RNAs (siRNA) in the moso bamboo (Zhou, Zhu, Bai, Hänninen, & Meng, 2017) that might contribute to diversification of gene regulatory network.…”