Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family‐specific impact on gene structure and genome organization

Abstract

SUMMARYShort interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

“…While median exon size (Fig. 6b) could reflect species-specific nucleosome sizes [76, 77], this does not explain why only the Hemiptera seldom exceed this (Fig. 6b: Q3 quartile).…”

“…Such small introns could be consistent with proliferation of non-autonomous short interspersed nuclear elements (SINEs). However, characterization of such highly divergent non-coding elements would require curated SINE libraries for insects, comparable to those generated for vertebrates and plants [76, 77]. Meanwhile, it appears that hemipteran open reading frames ≥160 bp are generally prevented by numerous in-frame stop codons just after the donor splice site.…”

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

“…For SINEs, a similar mechanism may be postulated because 30% of all SINE copies in Solanaceae genomes are associated with genes, very frequently in introns and untranslated regions (UTRs), and more than 10% of all genes contain at least one SINE insertion, with the extreme example of a metallophosphoesterase gene of pepper ( Capsicum sp.) which harbors 16 SINE copies (Seibt et al ., ). Therefore, we propose that DNA transposons and SINEs in sugar beet also influence gene expression in euchromatic gene‐rich regions (Menzel et al ., , ; Schwichtenberg et al ., ), because they might be targets for siRNA‐directed CHH methylation.…”

The conserved 3′ Angio‐domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants

“…Due to this, SINE annotations are often missing, incorrect, or incomplete. However, their annotation is highly relevant for gene characterization as many SINE families are enriched in or near genes, leading to changes in gene structure, regulation or splicing patterns (Ohtsubo et al , ; Tsuchimoto et al , ; Ben‐David et al , ; Seibt et al , ; Mao and Wang, ).…”

“…Within plants, SINE families have been first characterized in some species of Poales, Solanales, Brassicales, and Fabales (Mochizuki et al , ; Yoshioka et al , ; Deragon et al , ; Yasui et al , ; Gadzalski and Sakowicz, ). With the increasing availability of genome sequences a wide variety of plant species is accessible and bioinformatic algorithms such as the SINE‐Finder program (Wenke et al , ) enable the targeted identification of SINE families across the plant kingdom for comparative and evolutionary studies (Schwichtenberg et al , ; Seibt et al , ; Kögler et al , ; Mao and Wang, ).…”