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21 pages, 4816 KiB

Open AccessArticle

Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods

by Eliška Lukjanová, Alžběta Hanulíková and Jana Řepková

Plants 2023, 12(2), 235; https://doi.org/10.3390/plants12020235 - 04 Jan 2023

Cited by 1 | Viewed by 1430

Abstract

Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though [...] Read more.

Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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18 pages, 2874 KiB

Open AccessArticle

Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae)

by Olga V. Muravenko, Olga Yu. Yurkevich, Julia V. Kalnyuk, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk and Alexandra V. Amosova

Plants 2022, 11(17), 2244; https://doi.org/10.3390/plants11172244 - 29 Aug 2022

Cited by 2 | Viewed by 1937

Abstract

Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil [...] Read more.

Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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14 pages, 4682 KiB

Open AccessArticle

Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae

by Alexis J. Maravilla, Marcela Rosato, Inés Álvarez, Gonzalo Nieto Feliner and Josep A. Rosselló

Plants 2021, 10(12), 2794; https://doi.org/10.3390/plants10122794 - 17 Dec 2021

Cited by 4 | Viewed by 2211

Abstract

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR [...] Read more.

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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16 pages, 3896 KiB

Open AccessArticle

Plastome Diversity and Phylogenomic Relationships in Asteraceae

by Joan Pere Pascual-Díaz, Sònia Garcia and Daniel Vitales

Plants 2021, 10(12), 2699; https://doi.org/10.3390/plants10122699 - 08 Dec 2021

Cited by 14 | Viewed by 3293

Abstract

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven [...] Read more.

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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16 pages, 1743 KiB

Open AccessArticle

Variation in Ribosomal DNA in the Genus Trifolium (Fabaceae)

by Radka Vozárová, Eliška Macková, David Vlk and Jana Řepková

Plants 2021, 10(9), 1771; https://doi.org/10.3390/plants10091771 - 25 Aug 2021

Cited by 5 | Viewed by 2091

Abstract

The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to [...] Read more.

The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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Review

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24 pages, 2102 KiB

Open AccessEditor’s ChoiceReview

Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

by Natalia Borowska-Zuchowska, Magdalena Senderowicz, Dana Trunova and Bozena Kolano

Plants 2022, 11(6), 784; https://doi.org/10.3390/plants11060784 - 16 Mar 2022

Cited by 6 | Viewed by 2978

Abstract

Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the [...] Read more.

Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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18 pages, 4621 KiB

Open AccessReview

Advances in the Molecular Cytogenetics of Bananas, Family Musaceae

by Denisa Šimoníková, Jana Čížková, Veronika Zoulová, Pavla Christelová and Eva Hřibová

Plants 2022, 11(4), 482; https://doi.org/10.3390/plants11040482 - 11 Feb 2022

Cited by 7 | Viewed by 2784

Abstract

The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata [...] Read more.

The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata. It is worth mentioning that evolution and speciation in the Musaceae family were accompanied by large-scale chromosome structural changes, indicating possible reasons for lower fertility or complete sterility of these vegetatively propagated clones. Chromosomal changes, often accompanied by changes in genome size, are one of the driving forces underlying speciation in plants. They can clarify the genomic constitution of edible bananas and shed light on their origin and on diversification processes in members of the Musaceae family. This article reviews the development of molecular cytogenetic approaches, ranging from classical fluorescence in situ hybridization (FISH) using common cytogenetic markers to oligo painting FISH. We discuss differences in genome size and chromosome number across the Musaceae family in addition to the development of new chromosome-specific cytogenetic probes and their use in genome structure and comparative karyotype analysis. The impact of these methodological advances on our knowledge of Musa genome evolution at the chromosomal level is demonstrated. In addition to citing published results, we include our own new unpublished results and outline future applications of molecular cytogenetics in banana research. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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18 pages, 1993 KiB

Open AccessReview

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

by Alexis J. Maravilla, Marcela Rosato and Josep A. Rosselló

Plants 2021, 10(11), 2541; https://doi.org/10.3390/plants10112541 - 22 Nov 2021

Cited by 8 | Viewed by 2977

Abstract

The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available [...] Read more.

The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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17 pages, 1711 KiB

Open AccessReview

Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae)

by Eliška Lukjanová and Jana Řepková

Plants 2021, 10(11), 2518; https://doi.org/10.3390/plants10112518 - 19 Nov 2021

Cited by 5 | Viewed by 2650

Abstract

Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. [...] Read more.

Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes. Full article

(This article belongs to the Special Issue Plant Evolutionary Cytogenetics)

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