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1 The neoallohexaploid Senecio cambrensis (centre) flanked by its parents, tetraploid S. vulgaris (left) and diploid S. squalidus (right). Here, S. cambrensis has flower heads (capitula) of intermediate type to its parents; however, its ray florets can vary in length, and occasionally nonradiate forms (lacking ray florets) are also found in the wild
Source publication
Senecio cambrensis is one of a few allopolyploid plant species known to
have originated in the recent past and, therefore, provides excellent material for
analysing allopolyploid speciation. This allohexaploid species originated in the
UK within the last 100 years following hybridization between diploid S. squalidus
and tetraploid S. vulgaris. In t...
Citations
... Early allopolyploid evolution is well characterized in only a handful of plant systems, for example in the genera Cardamine (Zozomová-Lihová et al., 2014), Mimulus (Vallejo-Marin et al., 2015), Senecio (Hegarty et al., 2012), and Spartina (Aïnouche et al., 2004). Several allopolyploid taxa have been resynthesized, typically by treating homoploid hybrids between their parental taxa with colchicine (e.g., Comai et al., 2000;Tate et al., 2009;Szadkowski et al., 2010;Edger et al., 2017). ...
Premise:
Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time we compare phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids.
Methods:
Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness and analyzed differences between allopolyploids and their parental species and between synthetic and natural allopolyploids.
Key results:
As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to non-existent trait differences.
Conclusions:
In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization. This article is protected by copyright. All rights reserved.
... Polyploidisation strongly influences a number of morphological traits from cell size (Müntzing, 1936) to complex traits such as leaf and flower sizes and overall habit (Stebbins, 1971;Weiss-Schneeweiss et al., 2013;Č ertner et al., 2019). Because of their hybrid origin, allopolyploids show more pronounced changes in gene expression than autopolyploids (Hegarty et al., 2012), which may translate into more pronounced variation in physiological and morphological traits (Oates et al., 2012;Weiss-Schneeweiss et al., 2013). ...
... Intra-and interspecific hybridization is another mechanism that induces several types of genetic and epigenetic events that potentially lead to novel traits, new species, and increased invasiveness (104,237,242), which can affect the reproductive and growth potential of hybrids and 9. 10 Gioria et al. ...
Plant invasions, a byproduct of globalization, are increasing worldwide. Because of their ecological and economic impacts, considerable efforts have been made to understand and predict the success of non-native plants. Numerous frameworks, hypotheses, and theories have been advanced to conceptualize the interactions of multiple drivers and context dependence of invasion success with the aim of achieving robust explanations with predictive power. We review these efforts from a community-level perspective rather than a biogeographical one, focusing on terrestrial systems, and explore the roles of intrinsic plant properties in determining species invasiveness, as well as the effects of biotic and abiotic conditions in mediating ecosystem invasibility (or resistance) and ecological and evolutionary processes. We also consider the fundamental influences of human-induced changes at scales ranging from local to global in triggering, promoting, and sustaining plant invasions and discuss how these changes could alter future invasion trajectories.
Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... The 'Senecio system' is also rapidly becoming recognised as one of the most tractable plant models in which to study the process of speciation at a genetic, genomic, and ecological level (Abbott and Rieseberg, 2012;Gross, 2012;Walter et al., 2020). The fact that speciation events in the genus have occurred relatively recently, and involve examples of both ecological speciation and hybrid speciation (homoploid and allopolyploid; Abbott and Rieseberg, 2012;Hegarty et al., 2012), make Senecio a unique alternative to more conventional plant models, such as Arabidopsis, for studies of plant evolution in action. ...
... S. vulgaris is self-compatible with capitula that are rayless; whereas S. squalidus is self-incompatible with capitula showing a mix of ray and disc florets. Their hybridisation led to the evolution of an allohexaploid species, S. cambrensis, and tetraploid species, S. eboracensis (Lowe and Abbott, 2004;Brennan and Hiscock, 2010;Hegarty et al., 2012). Both hybrid species possess self-compatibility of S. vulgaris and ray florets from S. squalidus. ...
Many crop gene pools are derived from a small number of founders. As a consequence of long histories of strong directional selection, crop gene pools have narrow genetic diversity available to provide inherent solutions to changing needs or challenges. Notoriously, plants can mate across taxonomically-determined species boundaries, and interspecific hybridization is widely used in plant genetics research. Interspecific hybridizations have conferred practical improvements to crops, some of which are unexpected based on the phenotypes of the parents.
Genomics has provided insights into the fundamental consequences of interspecific hybridization for plant biology. Additionally, genomics has allowed the development of molecular tools for dissecting the genetic control of phenotypic variation in interspecific hybrid populations and manipulating interspecific introgressions in crop improvement.
This Research Topic aims to publish peer-reviewed research to interspecific hybridization and its consequences, both fundamental and applied. While such work is prominent in plants, consideration will also be given to salient work in other taxa. A key threshold for publication will be the extent to which findings are of cross-cutting interest and importance, i.e. not only to those working on the target taxon but to a wide range of biological scientists.
... The 'Senecio system' is also rapidly becoming recognised as one of the most tractable plant models in which to study the process of speciation at a genetic, genomic, and ecological level (Abbott and Rieseberg, 2012;Gross, 2012;Walter et al., 2020). The fact that speciation events in the genus have occurred relatively recently, and involve examples of both ecological speciation and hybrid speciation (homoploid and allopolyploid; Abbott and Rieseberg, 2012;Hegarty et al., 2012), make Senecio a unique alternative to more conventional plant models, such as Arabidopsis, for studies of plant evolution in action. ...
... S. vulgaris is self-compatible with capitula that are rayless; whereas S. squalidus is self-incompatible with capitula showing a mix of ray and disc florets. Their hybridisation led to the evolution of an allohexaploid species, S. cambrensis, and tetraploid species, S. eboracensis (Lowe and Abbott, 2004;Brennan and Hiscock, 2010;Hegarty et al., 2012). Both hybrid species possess self-compatibility of S. vulgaris and ray florets from S. squalidus. ...
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids’ point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
... HSE, also sometimes called homoeolog expression bias, has been observed in neopolyploids such as Senecio (Hegarty et al., 2012), mesopolyploids such as Gossypium (Adams et al., 2004;Chaudhary et al., 2009;Yoo et al., 2013), and even more broadly across polyploid plants (Buggs et al., 2010b;Grover et al., 2012;Woodhouse et al., 2014;Yang et al., 2016). Notably, we observed numerous loci demonstrating HSE, but overall, we see a similar proportion of loci exhibiting homoeolog expression bias toward each parent (Grover et al., 2012). ...
Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.
... In contrast, approximately 1362 and 1469 genes displayed expression divergence in two independently derived synthetic Arabidopsis allotetraploids, suggesting large-scale nonadditive gene regulation in the allotetraploids is due to interspecific hybridization [39]. Allopolyploids show earlier and more pronounced changes in gene expression than autopolyploids, which may cause more remarkable physiological and morphological variations [70,71]. Hybridization rather than genome doubling triggered gene expression changes resulting from cis-regulatory variation in cotton allopolyploids [72]. ...
Polyploidy is a pervasive and recurring phenomenon across the tree of life, which occurred at variable time scales, ecological amplitudes and cell types, and is especially prominent in the evolutionary histories of plants. Importantly, many of the world’s most important crops and noxious invasive weeds are recent polyploids. Polyploidy includes two major types, autopolyploidy, referring to doubling of a single species genome, and allopolyploidy referring to doubling of two or more merged genomes via biological hybridization of distinct but related species. The prevalence of both types of polyploidy implies that both genome doubling alone and doubling coupled with hybridization confer selective advantages over their diploid progenitors under specific circumstances. In cases of allopolyploidy, the two events, genome doubling and hybridization, have both advantages and disadvantages. Accumulated studies have established that, in allopolyploidy, some advantage(s) of doubling may compensate for the disadvantage(s) of hybridity and vice versa, although further study is required to validate generality of this trend. Some studies have also revealed a variety of non-Mendelian genetic and genomic consequences induced by doubling and hybridization separately or concertedly in nascent allopolyploidy; however, the significance of which to the immediate establishment and longer-term evolutionary success of allopolyploid species remain to be empirically demonstrated and ecologically investigated. This review aims to summarize recent advances in our understanding of the roles of hybridization and genome doubling, in separation and combination, in the evolution of allopolyploid genomes, as well as fruitful future research directions that are emerging from these studies.
... Species of Dendrosenecio exhibit 'mosaic of morphological variation' arising from divergence and convergence as they dispersed to various geographical regions with similar habitat conditions (Knox 2005;Mabberley 1973). Besides, frequent hybridization events between species within each genus have been evidenced resulting in allopolyploid species (Hedberg 1957;Hegarty et al. 2012;Milton 2009). It is therefore imperative that more molecular markers and divergent regions are identified to facilitate species identification, speciation and adaptive evolution studies on species of Senecio and Dendrosenecio. ...
Background:
Majority of the species within Senecioneae are classified in Senecio, making it the tribe's largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study.
Results:
The entire length of the complete chloroplast genomes was ~ 150 kb and ~ 151 kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio. A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea. A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade.
Conclusion:
Besides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera.
... Species of Dendrosenecio exhibit 'mosaic of morphological variation' arising from divergence and convergence as they dispersed to various geographical regions with similar habitat conditions (Knox 2005;Mabberley 1973). Besides, frequent hybridization events between species within each genus have been evidenced resulting in allopolyploid species (Hedberg 1957;Hegarty et al. 2012;Milton 2009). It is therefore imperative that more molecular markers and divergent regions are identified to facilitate species identification, speciation and adaptive evolution studies on species of Senecio and Dendrosenecio. ...
Podocarpus latifolius [(Thunb.) R.Br. ex Mirb.], also known as real yellow wood, is a large evergreen tree with exceptionally high-quality wood. It is a member of the Podocarpaceae family, which includes many species widely grown for wood pulp as well as timber for construction. Despite its importance, studies focusing on its genetic characterization and molecular biology are limited. Therefore, this study reports the complete plastome of P. latifolius , which is a circular molecule of 134 020 base pairs (bp) in length, lacking a quadripartite structure. The P. latifolius plastome encodes 117 unique genes, consisting of 82 protein-coding genes, 31 transfer RNA genes and four ribosomal RNA genes. The analysis showed that the Podocarpaceae plastomes have experienced some intron and gene losses, inversions, and inverted repeat (IR) loss resulting in a diverse plastome organization at the species and genus levels. Therefore, to understand the extent of these genomic rearrangements, more sampling of the Podocarpaceae plastomes is necessary. A total of 149 editing sites were predicted in 28 genes, all of which were C to U conversions. Moreover, a total of 164 simple sequence repeats (SSRs) were identified in the P. latifolius plastome, the majority being mononucleotide repeat motifs with A/T sequence predominance. Overall, the data obtained in this study will be useful for population genetics, evolutionary history and phylogenetic studies of the species in this genus.
... In the same study, the degree of HSE was additionally shown to increase with increasing time since polyploidization (Yoo et al. 2013). Genome expression biases also appear to occur in Senecio cambrensis, where bias was reproduced in natural and synthetic allopolyploids (Hegarty et al. 2012). Overall, there seems to be little consensus across allopolyploid plant species. ...
Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood. We describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogonmirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome.
