Distribution and Characteristics of Transposable Elements in the Mulberry Genome

Abstract

Core Ideas Percentage coverage of TEs is significantly negatively correlated with that of genes. Different TE superfamilies exhibit distinct distribution patterns in mulberry genome. Copia elements may have a dominant influence on the regulation of mulberry genes. TE‐containing genes assigned to pathways were mainly in metabolism‐related pathways. TEs are a driving force in the formation of alternatively spliced genes. Mulberry (Morus notabilis C. K. Schneid) leaves have been used as the food for the domesticated silkworm, Bombyx mori, for more than 5000 yr, and the mulberry–silkworm relationship is one of the best‐known and oldest models of plant defense–insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE‐rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The Copia elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE‐containing genes assigned to pathways were assigned to metabolism‐related pathways. The TE‐related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

“…This highlights the need for additional studies and sequencing of species of interest to investigate TE-associated polymorphisms, such as in P. sylvestris , which is an important species in northern Europe. In the two analyzed pine species, TE insertions were more often found in gene introns but less commonly in gene-flanking regions, similar to other plant species [ 150 , 151 , 152 , 153 ]. Insertions of TEs in gene regions are associated with various epigenetic mechanisms, but it remains unknown how some actively transcribed plant genes cope with large introns [ 140 ].…”

Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

“…In Coffea, Brachiaria, and Secale, for example, Gypsy probes were located in proximal heterochromatin-rich chromosome regions [17,57,58], but in Gossypium species, Gypsy probes were hybridized along chromosomes [59]. However, when the elements are considered according to their phylogenetic positions, i.e., lineages of Copia and Gypsy [5,7,60], it becomes evident that there are many differences in the TE distribution profiles, in both plants (see [10,61]) and animals [62,63]. Thus, it seems wiser to believe that each element has its characteristics, including chromosomal position, genome impact, epigenetic influence, diversification rate, and other features.…”

“…Files were used to search for autonomous and non-autonomous LTR-RTs. For genomic comparisons, a database was built to run a local BLAST, which contained all the TEs conserved protein sequences from REXdb [5], GypsyDB [61], RepBase [70] and NCBI (http://www.ncbi.nlm.nih.gov/), containing 283,676 protein sequences. To identify the rDNA sequences, a second database was compiled comprising nucleotides 35S and 5S rDNA sequences from different organisms, obtained from NCBI, containing 1652 sequences.…”

Comparative study of pine reference genomes reveals transposable element interconnected gene networks

“…This highlights the need for additional studies and sequencing of species of interest to investigate TE-associated polymorphisms, such as in P. sylvestris, which is an important species in northern Europe. In the two analyzed pine species, TE insertions were more often found in gene introns but less commonly in gene anking regions, similar to other plant species (West et al, 2014;Le et al, 2015;Li et al, 2017a;Ma et al, 2019). Insertions of TEs in gene regions are associated with various epigenetic mechanisms, but it remains unknown how some actively transcribed plant genes are coping with large introns (To et al, 2015).…”