Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events

Rosato, Marcela; Moreno-Saiz, Juan Carlos; Galián, José; Rosselló, Josep A.

doi:10.1093/aobpla/plv135

Cited by 17 publications

(11 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This indicates that while the 5S locus is always located on the same chromosome with one of the 45S rDNA loci, their sequences evolved independently. Independent evolution of both arrays was also reported in other plants and in animals (Rosato et al, 2015;Araya-Jaime et al, 2020).…”

Section: Features and Molecular Evolution Of Rdna Sequencessupporting

confidence: 68%

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)

et al. 2021

View full text Add to dashboard Cite

Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.

show abstract

Section: Features and Molecular Evolution Of Rdna Sequencessupporting

confidence: 68%

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Indeed, increasing number (and diversity) of the 5S lineages from V. kitaibeliana and V. hymettia (2 n = 16) to V. arvensis (2 n = 34) and V. tricolor (2 n = 26) is consistent with different and reiterated allopolyploidization events and subsequent genome restructuring with partial loss of 5S loci bearing chromosomes. It is interesting to note that similar dynamic and complex changes in rDNA genomic organization during speciation processes have been inferred in other plant systems as well, highlighting a general decoupling of the 5S rDNA loci number with polyploidization events and chromosome numbers, a fact that could be explained by locus loss or homogenization of 5S rDNA in allopolyploids over longer evolutionary times [ 51 , 77 ]. Therefore, the rate to which dysploidy affects the 5S loci bearing chromosomes in sect.…”

Section: Discussionmentioning

confidence: 75%

Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae (Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation

Scoppola

Cardoni

Marcussen

et al. 2022

Plants

View full text Add to dashboard Cite

Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal ‘V. tricolor species complex’: V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium.

show abstract

“…Dynamic and complex changes have been documented in their evolutionary history regarding the amplification and deletion of repeats and loci involving chromosome repatterning. Ran et al, 2001;Mishima et al, 2002;Weiss-Schneeweiss et al, 2008;Rosato et al, 2015;Totta et al, 2017 The number, genomic location and activity of 35S rDNA loci are constant within species…”

Section: Assumption Comments Selected Referencesmentioning

confidence: 99%

“…Pikaard, 2000a;González-Melendi et al, 2005;Rosato and Rosselló, 2009 Complexity may arise in lineages, however, when mechanisms involved in altering the number of rDNA loci have occurred along their evolutionary history. These bursts of rDNA amplification include the dispersion of loci by structural chromosome rearrangements at homoploid levels as well as the transposition and amplification of rDNA copy numbers (Datson and Murray, 2006;Rosato et al, 2017), and have involved both diploid lineages and complex scenarios of ancestral and more recent polyploid events (Rosato et al, 2015). These events may have resulted in karyotypes that eventually contain more 35S rDNA sites than expected when compared to the ancestral or parental lineages.…”

Section: Assumption Comments Selected Referencesmentioning

confidence: 99%

The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies

2022

Self Cite

View full text Add to dashboard Cite

The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.

show abstract

Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events

Cited by 17 publications

References 45 publications

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)

Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae (Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation

The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies

Contact Info

Product

Resources

About