Diverse evolutionary pathways shaped 5S rDNA of species of tribe Anemoneae (Ranunculaceae) and reveal phylogenetic signal

Abstract

Anemone sensu lato (including Pulsatilla and Hepatica), tribe Anemoneae (Ranunculaceae), is arranged into two subgenera, Anemone and Anemonidium, with basic chromosome numbers x = 8 and x = 7, respectively. We elucidated the level of divergence of 5S rDNA unit arrays between the subgenera, determined intra‐individual and interspecific sequence variation and tested 5S rDNA phylogenetic signal in revealing the origin of polyploid species. High intra‐individual nucleotide diversity and the presence of 5S rDNA unit array length variants and pseudogenes indicate that weak homogenization forces have shaped 5S rDNA in the investigated species. Our results show that 5S rDNA evolved through two major changes: diversification of 5S rDNA into two lineages, one with long (subgenus Anemone) and one with short 5S rDNA unit arrays (subgenus Anemonidium); and subsequent contraction and expansion of 5S rDNA unit arrays. Phylogenetic analysis based on 5S rDNA supports the hypothesis that A. parviflora could be a parental species and donor of the subgenome D to the allopolyploids A. multifida (BBDD) and A. baldensis (AABBDD). In A. baldensis interlocus exchange possibly occurred, followed by subsequent replacement of the 5S rDNA from subgenome D with those from subgenome B. Here we present evidence that both models, concerted and birth‐and‐death evolution, were probably involved in the evolution of the 5S rDNA multigene family in subgenera Anemone and Anemonidium.

High‐throughput sequencing of 5S‐IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples

“…Observed intraspecific, interspecific and intra‐individual polymorphism of the intergenic spacer of the 5S cistron in Quercus (in terms of unit length, GC content and nucleotide sequence) is consistent with many other plant groups (Forest et al., 2005; Fulnecěk et al., 2002; Grimm & Denk, 2010; Mahelka et al., 2013; Mlinarec et al., 2016; Negi et al., 2002; Tynkevich & Volkov, 2019). The intra‐individual and/or intraspecific occurrence of two (or more) distinct 5S array types (e.g., “short” and “long” units in members of sect.…”

“…The 5S rRNA genes form gene arrays analogous to the 35S rDNA, localized on one or a few chromosomes, usually far from the nucleolus organizer regions (NORs) of the 35S rDNA (http://www.plantrdnadatabase.com/; see Ribeiro et al., 2011 for selected oak and beech species). In higher plants, the number of repeats per genome ranges from hundreds to thousands (Cloix et al., 2000), and the 5S rRNA coding regions are separated by a generally variable, nontranscribed intergenic spacer (5S‐IGS) with high phylogenetic resolution (e.g., Blattner, 2009; Forest et al., 2005; Garcia & Kovařik, 2013; Grimm & Denk, 2010; Mlinarec et al., 2016). Its interindividual and intragenomic variability is probably the main reason why it is little used.…”

5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

“…However, it was found that the IGS of Arabidopsis thaliana contains short-sequence motifs involved in initiation (external elements of the promoter) and termination (terminator) of 5S rDNA transcription ( Douet and Tourmente, 2007 ; de Souza et al, 2020 ). Thus, one would expect that these regions are to be relatively conservative, as has been demonstrated in several taxonomic groups ( Falistocco et al, 2007 ; Tynkevich and Volkov, 2014 ; Tynkevich et al, 2015 ; Mlinarec et al, 2016 ; Ishchenko et al, 2018 ; Alexandrov et al, 2021 ). However, the existing knowledge of the organization of external promoter elements and their molecular evolution is still incomplete.…”

“…Additive inheritance of both parent variants of 5S and 35S rDNA is usually observed in the first generation of interspecific hybrids/allopolyploids. However, in ancient allopolyploids, 35S rDNA can be the subject of interlocus sequence conversion ( Volkov et al, 1999a , b , 2007 ; Vizoso et al, 2011 ), while different variants of 5S rDNA can coexist in a plant genome for a long time without being homogenized ( Fulnecek et al, 2002 ; Song et al, 2012 ; Mahelka et al, 2013 ; Mlinarec et al, 2016 ; Volkov et al, 2017 ; Ishchenko et al, 2018 ). Especially, a significant sequence divergence was found for spatially distant 5S rDNA variants that are located in different loci of the same chromosome set ( Cronn et al, 1996 ; Vozárová et al, 2021 ) and for different parent loci in genomes of hybrid origin ( Fulnecek et al, 2002 ; Matyasek et al, 2002 ), while repeats from the same locus appeared to be highly homogenized.…”

Subrepeats in 5s rDNAs as a molecular marker in Acer platanoides L. populations

“…Кодувальна ділянка є еволюційно консервативною, і помітна різниця в її послідовності спостерігається лише за порівняння віддалених таксонів. Натомість, послідовність МГС швидко накопичує мутації і нерідко значно відрізняється вже на міжвидовому або міжпопуляційному рівні [7,[14][15][16][17][18][19].…”