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Advances in Genome Size Evolution of Plants

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 29917

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Special Issue Editors

Dr. Sonja Siljak-Yakovlev

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Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
Interests: chromosome evolution and genome organization; cytogenetics and evolution of plants; biodiversity; endemism

Dr. Oriane Hidalgo

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Guest Editor

Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
Interests: Asteraceae; biodiversity; genome evolution; plant reproductive morphologies

Prof. Joan Vallès

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Guest Editor

Laboratori de Botànica (UB) - Unitat associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
Interests: Asteraceae; cytogenetics; plant systematics and evolution

Special Issue Information

Dear Colleagues,

Genome size, the amount of DNA in a somatic unreplicated nucleus (2C), is one of the most fundamental biological characteristics of living organisms. It was originally described as C-value, referring to the DNA content of the unreplicated gametic chromosome set of an organism, which was considered characteristic and invariable (the C accounting for ‘constant’) within a species. However, evidence for intraspecific genome size variation has increasingly been reported. Knowledge on genome size is useful in many disciplines such as ecology and phytogeography, systematics and evolution, biotechnology and agronomical sciences, and also in biodiversity screening. Furthermore, in the age of genomics, C-values provide baseline yet critical data for DNA sequencing projects, including emerging full-genome sequencing.

Much effort has been made to investigate the origin, extent, and biological significance of genome size diversity across land plants, and two processes are mainly responsible for such variation: (i) chromosome rearrangements and differential amplification in the amount of repetitive DNA inducing changes on the monoploid genome size (1Cx, DNA content of a monoploid genome with chromosome base number x); (ii) whole genome multiplication or polyploidization frequently involving a duplication of the DNA content.

Plants stand out amongst eukaryotes for presenting a staggering genome size range of ca. 2400-fold, the largest for any comparable group of organisms. However, genome size has been estimated for only 3.1% of the ca. 350,000 species of angiosperms, the largest plant group, with the coverage in plants ranging from 1.7% in mosses (ca. 12,000 species) to 41% in gymnosperms (ca. 1000 species). It is becoming increasingly evident that genome size influences plants in myriad ways at the nuclear, cellular, and whole plant levels, ultimately affecting species evolvability and resilience to environmental change. The growing pool of available genome size data together with recent advances and improvements in methodological and statistical approaches make it possible to gain critical insights into genome size dynamics.

This Special Issue aims at contributing to this topic through a wide range of articles (original research papers, perspectives, hypotheses, reviews, modeling approaches and methods) on genome size diversity and evolution in plants.

Dr. Sonja Siljak-Yakovlev
Dr. Oriane Hidalgo
Prof. Joan Vallès
Guest Editors

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Keywords

ancestral genome size reconstruction
changes in genome size
distribution of genome sizes
genome size diversification
genome size evolution
genome size dynamics

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Research

9 pages, 951 KiB

Open AccessArticle

Genome Size Variation Assessment in Vitis vinifera L. Landraces in Ibiza and Formentera (Balearic Islands)

by Raquel González, Joan Vallès and Teresa Garnatje

Plants 2022, 11(14), 1892; https://doi.org/10.3390/plants11141892 - 21 Jul 2022

Cited by 4 | Viewed by 1675

Abstract

Plant genome size has many applications in different biological fields including ecology and plant breeding. The 2C value for Vitis vinifera L. has not been widely studied; furthermore, to date, no data from local landraces in the Pityusic Islands (the two smaller inhabited Balearic Islands, Ibiza, and Formentera) have been reported. This research aims to contribute to this knowledge and investigate whether there are variations between different grape landraces cultivated in Ibiza and Formentera and also among the same landraces on each island. To this end, 36 accessions of 15 cultivars and 6 landraces, identified with SSR markers, were assessed using flow cytometry. The results revealed that 2C values ranged from 1.09 pg to 1.28 pg. There were statistically significant differences in ‘AG1’ and ‘AG2’ landraces and ‘Santa Magdalena’, ‘Garnatxa’, ‘Danugue’, and ‘Valencí tinto/Grumier’ cultivars. No statistically significant differences were found in terms of the genome size content between islands. Statistically significant differences were found in accessions within ‘AG2’ landrace group and ‘Beba’ cultivar. The results presented here constitute the first-ever reported information on genome size in the genus Vitis vinifera in Pityusic, Balearic, and, in general, Spanish accessions, and they are one of the largest prospections in this field for this species anywhere. Further research should be conducted to explain the differences in nuclear DNA content found between landraces and cultivars studied here with others cultivated in different islands or countries to understand whether genome size varies in modern cultivars compared with local landraces. Additionally, it would be interesting to investigate whether there is a relationship between genome size and adaptations to diverse climatology conditions, crop management, and ripening characteristics. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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16 pages, 2739 KiB

Open AccessEditor’s ChoiceArticle

Genome Size Variation in Dianthus sylvestris Wulfen sensu lato (Caryophyllaceae)

by Ana Terlević, Sandro Bogdanović, Božo Frajman and Ivana Rešetnik

Plants 2022, 11(11), 1481; https://doi.org/10.3390/plants11111481 - 31 May 2022

Cited by 15 | Viewed by 2883

Abstract

Genome size (GS) is an important characteristic that may be helpful in delimitation of taxa, and multiple studies have shown correlations between intraspecific GS variation and morphological or environmental factors, as well as its geographical segregation. We estimated a relative GS (RGS) of 707 individuals from 162 populations of Dianthus sylvestris with a geographic focus on the Balkan Peninsula, but also including several populations from the European Alps. Dianthus sylvestris is morphologically variable species thriving in various habitats and six subspecies have been recognized from the Balkan Peninsula. Our RGS data backed-up with chromosome counts revealed that the majority of populations were diploid (2n = 30), but ten tetraploid populations have been recorded in D. sylvestris subsp. sylvestris from Istria (Croatia, Italy). Their monoploid RGS is significantly lower than that of the diploids, indicating genome downsizing. In addition, the tetraploids significantly differ from their diploid counterparts in an array of morphological and environmental characteristics. Within the diploid populations, the RGS is geographically and only partly taxonomically correlated, with the highest RGS inferred in the southern Balkan Peninsula and the Alps. We demonstrate greater RGS variation among the Balkan populations compared to the Alps, which is likely a result of more pronounced evolutionary differentiation within the Balkan Peninsula. In addition, a deep RGS divergence within the Alps likely points to persistence of the alpine populations in different Pleistocene refugia. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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15 pages, 5044 KiB

Open AccessArticle

Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps

by Pol Fernández, Oriane Hidalgo, Ana Juan, Ilia J. Leitch, Andrew R. Leitch, Luis Palazzesi, Luca Pegoraro, Juan Viruel and Jaume Pellicer

Plants 2022, 11(9), 1235; https://doi.org/10.3390/plants11091235 - 2 May 2022

Cited by 6 | Viewed by 2387

Abstract

Polyploidy is a widespread phenomenon across angiosperms, and one of the main drivers of diversification. Whilst it frequently involves hybridisation, autopolyploidy is also an important feature of plant evolution. Minority cytotypes are frequently overlooked due to their lower frequency in populations, but the development of techniques such as flow cytometry, which enable the rapid screening of cytotype diversity across large numbers of individuals, is now providing a more comprehensive understanding of cytotype diversity within species. Senecio doronicum is a relatively common daisy found throughout European mountain grasslands from subalpine to almost nival elevations. We have carried out a population-level cytotype screening of 500 individuals from Tête Grosse (Alpes-de-Haute-Provence, France), confirming the coexistence of tetraploid (28.2%) and octoploid cytotypes (71.2%), but also uncovering a small number of hexaploid individuals (0.6%). The analysis of repetitive elements from short-read genome-skimming data combined with nuclear (ITS) and whole plastid DNA sequences support an autopolyploid origin of the polyploid S. doronicum individuals and provide molecular evidence regarding the sole contribution of tetraploids in the formation of hexaploid individuals. The evolutionary impact and resilience of the new cytotype have yet to be determined, although the coexistence of different cytotypes may indicate nascent speciation. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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14 pages, 2883 KiB

Open AccessArticle

Cytogenetic, Morphometric, and Ecological Characterization of Festuca indigesta Boiss. in the Southeast of Spain

by Gloria Martínez-Sagarra, Federico Casimiro-Soriguer, Sílvia Castro, João Loureiro and Juan A. Devesa

Plants 2022, 11(5), 693; https://doi.org/10.3390/plants11050693 - 4 Mar 2022

Cited by 1 | Viewed by 2419

Abstract

Festuca indigesta subsp. indigesta (Poaceae) is endemic to the southeast of Spain, and until recently, it was considered that its range of distribution was restricted to the siliceous core of Sierra Nevada. However, it has been recently extended in the territory to others calcareous mountains. This study investigates the cytogenetic variability throughout the geographic range of this taxon, the possible edaphic preferences of each cytotype, and the morphological variation of cytotypes. Genome sizes and ploidy levels were estimated using flow cytometry and chromosome count. Soil samples were collected to test the nature of the substrate, i.e., pH, and calcium and magnesium contents. Finally, morphological characters were measured in herbarium specimens. This study provides the first genome size data for the species. Hidden cytogenetic diversity was detected in the taxon, comprising hexaploid (2n = 6x = 42), octoploid (2n = 8x = 56) and dodecaploid (2n = 12x = 84) individuals. No relationship between substrate nature and cytotype was observed. Morphological differences were detected for the size of floral parts and stomata among cytotypes, but these were blurred if the entire morphological variation range was considered. Our results suggest that each mountain range could act as a reservoir of morphologically cryptic genetic diversity regarding this taxon. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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15 pages, 2643 KiB

Open AccessArticle

Genome Size and Chromosome Number Evaluation of Astragalus L. sect. Hymenostegis Bunge (Fabaceae)

by Ali Bagheri, Azadeh Akhavan Roofigar, Zahra Nemati and Frank R. Blattner

Plants 2022, 11(3), 435; https://doi.org/10.3390/plants11030435 - 5 Feb 2022

Cited by 3 | Viewed by 2924

Abstract

Astragalus section Hymenostegis is one of the important characteristic elements of thorn-cushion formations in the Irano-Turanian floristic region. In this paper, we examined the chromosome number of 17 species (15 new reports) and provide estimates of genome size for 62 individuals belonging to 38 taxa of A. sect. Hymenostegis, some species outside this section, plus two Oxytropis species. Based on chromosome counts 11 species were found to be diploid (2n = 16), four species tetraploid (2n = 32) and two taxa hexaploid (2n = 48). From genome size measurements on silica-gel dried material, three ploidy levels (2x, 4x and 6x) were inferred, with a majority of species being diploid. The 2C values reach from 2.07 pg in diploid Astragalus zohrabi to 7.16 pg in hexaploid A. rubrostriatus. We found indications that species might occur with different cytotypes. A phylogenetic framework using nrDNA ITS sequences was constructed to understand the evolution of ploidy changes and genome sizes. It showed that genome size values among the studied taxa differ only slightly within ploidy levels and are nearly constant within most species and groups of closely related taxa within the genus Astragalus. The results of this study show that there is a rather strong correlation between genome sizes and chromosome numbers in sect. Hymenostegis. The resolution of the ITS-based phylogenetic tree is too low to infer evolutionary or environmental correlations of genome size differences. Polyploidization seems to contribute to the high species number in Astragalus, however, in sect. Hymenostegis it is not the main driver of speciation. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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13 pages, 2059 KiB

Open AccessArticle

Genome Size of Life Forms of Araceae—A New Piece in the C-Value Puzzle

by Domen Kocjan, Jasna Dolenc Koce, Florian Etl and Marina Dermastia

Plants 2022, 11(3), 334; https://doi.org/10.3390/plants11030334 - 27 Jan 2022

Cited by 4 | Viewed by 4407

Abstract

The genome size of an organism is an important trait that has predictive values applicable to various scientific fields, including ecology. The main source of plant C-values is the Plant DNA C-values database of the Royal Botanic Gardens Kew, which currently contains 12,273 estimates. However, it covers only 2.9% of known angiosperm species and has gaps in the life form and geographic distribution of plants. Only 4.5% of C-value estimates come from researchers in Central and South America. This study provides 41 new C-values for the aroid family (Araceae), collected in the Piedras Blancas National Park area in southern Costa Rica, including terrestrial, epiphytic and aquatic life forms. Data from our study are combined with C-value entries in the RBGK database for Araceae. The analysis reveals a wider range of C-values for terrestrial aroids, consistent with other terrestrial plants, a trend toward slightly lower C-values for epiphytic forms, which is more consistent for obligate epiphytes, and comparatively low C-values for aquatic aroids. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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15 pages, 1889 KiB

Open AccessArticle

Morphological and Genome-Wide Evidence of Homoploid Hybridisation in Urospermum (Asteraceae)

by Jaume Pellicer, Manica Balant, Pol Fernández, Roi Rodríguez González and Oriane Hidalgo

Plants 2022, 11(2), 182; https://doi.org/10.3390/plants11020182 - 11 Jan 2022

Cited by 5 | Viewed by 2783

Abstract

The genus Urospermum is distributed in the Mediterranean region and Macaronesia, and has been introduced to other extra-Mediterranean regions. Although the two species constituting the genus, U. dalechampii and U. picroides, are frequently found together, hybrids have so far only been reported once, from Morocco. However, we found certain individuals in Catalonia, whose intermediate morphology suggested a potential hybrid origin. In this study, we applied morphological and molecular methods to investigate the origin of those individuals. Intermediate features at phenotype, karyological, cytogenetic, and genomic levels were identified in morphologically intermediate individuals, supporting their homoploid hybrid origin. Chloroplast sequence data suggest that U. dalechampii is the maternal progenitor of the hybrid. Together with the intermediate traits displayed, the lack of fertile seeds suggests that hybrids are probably F1. Future monitoring studies will be, nonetheless, needed to evaluate the extent of hybridisation and its potential impact on the biology of the genus. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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18 pages, 1743 KiB

Open AccessFeature PaperArticle

Genome Size, Cytotype Diversity and Reproductive Mode Variation of Cotoneaster integerrimus (Rosaceae) from the Balkans

by Faruk Bogunić, Sonja Siljak-Yakovlev, Irma Mahmutović-Dizdarević, Alma Hajrudinović-Bogunić, Mickaël Bourge, Spencer C. Brown and Edina Muratović

Plants 2021, 10(12), 2798; https://doi.org/10.3390/plants10122798 - 17 Dec 2021

Cited by 6 | Viewed by 3099

Abstract

Cotoneaster integerrimus represents a multiploid and facultative apomictic system of widely distributed mountain populations. We used flow cytometry to determine genome size, ploidy level, and reproduction mode variation of the Balkan populations, supplemented by analysis of nuclear microsatellites in order to address: (i) geographic distribution and variation of cytotypes among the populations; (ii) variation of reproduction mode and the frequency of sexuality; (iii) pathways of endosperm formation among the sampled polyploids and their endosperm balance requirements; (iv) genotypic diversity and geographic distribution of clonal lineages of polyploids. The prevalence of apomictic tetraploid cytotype followed by sexual diploids and extremely rare triploids was demonstrated. This prevalence of tetraploids affected the populations’ structure composed from clonal genotypes with varying proportions. The co-occurrence of diploids and tetraploids generated higher cytotype, reproductive mode, and genotypic diversity, but mixed-ploidy sites were extremely rare. The endosperm imbalance facilitates the development and the occurrence of intermediate triploids in mixed-ploidy populations, but also different tetraploid lineages elsewhere with unbalanced endosperm. All these results showed that the South European populations of C. integerrimus have higher levels of cytotype and reproductive diversity compared to the Central European ones. Therefore, the South European populations can be considered as a potential reservoir of regional and global diversity for this species. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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10 pages, 1997 KiB

Open AccessArticle

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

by Bokyung Choi, Geun-Hye Gang, Hyeonjin Kim, Hyejoo Byun, Minyeong Kwak, Soonku So, Hyeon-Ho Myeong and Tae-Soo Jang

Plants 2021, 10(10), 1978; https://doi.org/10.3390/plants10101978 - 22 Sep 2021

Cited by 6 | Viewed by 2668

Abstract

Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady’s slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady’s slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady’s slipper orchid species. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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9 pages, 1181 KiB

Open AccessCommunication

Detecting Introgressed Populations in the Iberian Endemic Centaurea podospermifolia through Genome Size

by Jaume Pellicer, Jordi López-Pujol, Marc Aixarch, Teresa Garnatje, Joan Vallès and Oriane Hidalgo

Plants 2021, 10(8), 1492; https://doi.org/10.3390/plants10081492 - 21 Jul 2021

Cited by 6 | Viewed by 2390

Abstract

Based on results from previous studies, populations of the Iberian endemic Centaurea podospermifolia north of the Ebro River are considered genetically pure, while those southward are introgressed, with genetic input from C. cephalariifolia. This phenomenon is particularly relevant, especially given both the endangered and protected status for the species, which can have consequences in how to best apply conservation strategies to maintain genetic resources in the species. The main goal of this study was to evaluate whether genome size assessments using flow cytometry can help distinguishing between pure, hybrid and introgressed populations, and hence become a powerful and cost-effective tool to complement comprehensive population genetic surveys. The results indicate that there are significant genome size differences between populations of C. podospermifolia, which are coincident with previous considerations of pure and introgressed populations. Given the simplicity and reproducibility of this technique, flow cytometry could become an effective tool for monitoring pure populations of this species and, indeed, become an integral part of the management plans that are mandatory for listed taxa. Full article

(This article belongs to the Special Issue Advances in Genome Size Evolution of Plants)

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