5S-IGS rDNA in wind-pollinated trees (<i>Fagus</i>L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

Cardoni, Simone; Piredda, Roberta; Denk, Thomas; Grimm, Guido W.; Ac, Papageorgiou; Schulze, Ernst Detlef; Scoppola, Anna; Ps, Shanjani; Suyama, Yoshihisa; Tomaru, Nobuhiro; Worth, James R. P.; Mc, Simeone

doi:10.1101/2021.02.26.433057

Cited by 3 publications

(1 citation statement)

References 126 publications

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“…Recent phylogenetic studies have revealed that these three species belong to the same lineage, F. crenata-F. sylvatica s. l., which diverged from the remaining Asian lineage of the subgen. Fagus in the Middle Eocene (Cardoni et al, 2021;Renner et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Review: Phytogeography and history of Japanese beech forests: Recent advances and implications for vegetation ecology

Hara

2022

Ecological Research

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In this review, the phytogeography and history of Japanese beech (Fagus crenata Blume and F. japonica Maxim.) forests are re‐examined in light of recent phytogeographical and palaeobotanical research advances. I explain the floristics and the climatic and geological contrasts between Japanese beech forests on the Sea of Japan side and the Pacific side of the Japanese archipelago. We also review recent studies on the origin of dwarf evergreen shrub species occurring along the Sea of Japan. The old scenario that these dwarf evergreen shrub species diverged directly from counterpart species occurring on the Pacific coast of Japan is no longer supported. We propose more intricate speciation processes, including phylogenetic relations to extant Chinese species and inter‐species hybridization. We also review the results of recent palaeobotanical studies of forests on the Japanese islands in the Quaternary. The long persistence of beech forests through glacial/interglacial cycles of the Quaternary—with repeated spread and contraction of the geographical range—is confirmed. In addition, we briefly explain the phytosociological classification system of the Japanese beech forest and the geographical ranges of each vegetation type. We review studies of the geographic distribution of F. crenata and F. japonica at the population level, highlighting the need for further ecological and genetic studies of population dynamics near the range limits to understand historic migration processes better.

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Section: Introductionmentioning

confidence: 99%

Review: Phytogeography and history of Japanese beech forests: Recent advances and implications for vegetation ecology

Hara

2022

Ecological Research

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

et al. 2022

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The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.

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Organization and polymorphysm of 5S rDNA intergenic spacer of blackthorn (Prunus spinosa L.)

Tynkevich¹,

Kozub²,

Волков³

2021

Visn. ukr. tov. genet. sel.

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Aim. The 5S rDNA repeated units consist of conserved regions encoding 5S rRNA and variable intergenic spacers (IGS). The IGS sequences are commonly used as molecular markers for low-ranking phylogenetic, phylogeographical and microevolutionary studies. However, this genomic region still remains undescribed for the waist majority of genera in the Rosaceae family. Here we present the first report of the IGS molecular organization and polymorphism for the widespread member of the Rosaceae family, Prunus spinosa. Methods. PCR amplification, cloning and sequencing of 5S rDNA, bioinformatics analysis. Results. The 5SrDNA IGS of P. spinosa was cloned sequenced and compared with the IGS of three other representatives of the genus Prunus. It was found that the IGS variants present in the genome of P. spinosa differ by the number of subrepeats located at the 5’end. Each of these subrepeats contain RNA Pol III transcription termination signal. The IGS sequences of Prunus species evolved mainly by accumulation of nucleotide substitutions. The level of intragenomic similarity of P. spinosa IGS is 96.5-100%, while the similarity between the IGS of different Prunus species ranges from 73.0 to 87.3%. Conclusions. The IGS of 5S rDNA represents a useful marker for phylogenetic and taxonomic studies in the genus Prunus.Keywords: 5S rDNA, molecular evolution, Prunus spinosa.

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5S-IGS rDNA in wind-pollinated trees (FagusL.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

Cited by 3 publications

References 126 publications

Review: Phytogeography and history of Japanese beech forests: Recent advances and implications for vegetation ecology

Review: Phytogeography and history of Japanese beech forests: Recent advances and implications for vegetation ecology

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

Organization and polymorphysm of 5S rDNA intergenic spacer of blackthorn (Prunus spinosa L.)

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