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Polyploidy is a pervasive phenomenon in nature and has significantly contributed to the adaptive evolution of plants. The conditions necessary for the spread of neopolyploids in populations of the diploid progenitor are limited; however, the superior competitive ability of neopolyploids may promote its establishment. Here, we assess the contribution of polyploidisation to the divergence of plant traits affecting competitive response, which could explain the successful establishment and current geographic distribution of polyploids. We conducted an intraspecific competition experiment using diploids, neotetraploids and established tetraploids of Jasione maritima var. maritima to determine whether cytotypes differ in phenological, growth and physiological traits and competitive response. Cytotypes respond differently under different competition scenarios with implications for cytotype establishment and distribution. Competition impacted all cytotypes, but neotetraploids were least affected by competition, and the tetraploids were the most impacted. Thus, competitive advantage may have contributed to the displacement of diploid populations and colonisation of new areas by neotetraploids but might have been lost afterwards. Evolutionary changes after polyploidisation have also been detected, and tetraploids invested more in belowground biomass, suggesting that root development might also play a role in colonising southernmost locations. Interestingly, diploids and both tetraploids seem to have different life strategies, the first investing in growth while the latter investing in reserves for the next season. Overall, polyploidisation seems to provide immediate changes that confer an advantage under competition that, together with other factors, may have allowed the establishment of neotetraploids. [ABSTRACT FROM AUTHOR]

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes. [ABSTRACT FROM AUTHOR]

Vertebrates, often considered as the most sophisticatedly organized animals, have a number of unique morphological features that ensured their evolutionary stability and success. Many have argued that the genetic basis for these innovations was provided by the genome duplications occurred at the early stages of vertebrate evolution. One of the important results of genome duplication is the emergence of additional copies of regulatory genes. Having been removed from the constraining pressure of natural selection, these copies acquired an opportunity to modify their structure and functions, influencing the organism's development and morphology. The consequence of ancient genomic duplications is, for example, that about 35% of human genes are represented by at least two homologous copies. The idea of genome duplications occurred at the early stages of vertebrate evolution was first proposed in 1970, but questions about the number, the scale (whole-genome or local) and the evolutionary timing of these duplications are still actively debated. In recent years (2018–2020), due to the rapid development of methods for processing of big data of high-throughput genome sequencing in different lineages of vertebrates and their closest relatives, cephalochordates and tunicates, a number of comparative studies aimed at identifying groups of syntheny in genomes of different evolutionary lines and reconstruction of ancestral vertebrate chromosomes were obtained. As a result, several models describing putative scenarios of genome duplications in vertebrate evolution have been proposed. In parallel, detailed laboratory studies focused on the expression and functional properties of different families of regulatory genes were performed for representatives of several vertebrate groups. In these studies, a plethora of new information on the molecular mechanisms of the embryonic development in hitherto poorly studied representatives of the evolutionarily ancient vertebrate linages (e.g. cyclostomes, cartilaginous fishes and sturgeons) have been collected. In this review, we consider modern concepts of the mechanisms and consequences of genomic duplications in the light of recent experimental data and currently proposed models of vertebrate genome evolution. [ABSTRACT FROM AUTHOR]

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma ) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes., Competing Interests: Competing interests statement:The authors declare no competing interest.

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species. [ABSTRACT FROM AUTHOR]

Vertebrates appear about 500 million years ago in the fossil record. This is only 25–50 million years after the great explosion of multicellular invertebrate body plans in the early Cambrian. On a geological time scale, this interval is a ‘blink of an eye’, suggesting that the evolution of regulatory genes is likely to be important in the origins of vertebrates. Here we present evidence for a role of steroid receptors in this process based on a phylogenetic analysis suggesting that receptors for androgens, glucocorticoids, mineralocorticoids, and progesterone evolved from an ancestral steroid receptor gene by two successive duplications over a brief time that could have coincided with the origins of vertebrates. Moreover, the duplications of these steroid receptors may be additional evidence for the two duplications on a genome-scale that have been proposed to be important in the evolution of vertebrates. The two successive duplications of steroid receptor genes and their subsequent sequence divergence leading to steroid-specific receptors that regulate growth, development, reproduction and homeostasis in vertebrates may have been one of the events important in vertebrate survival after the Cambrian during global extinctions that occurred about 440 and 370 million years ago.

Natural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora ( Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region. [ABSTRACT FROM AUTHOR]

All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.

All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype. [ABSTRACT FROM AUTHOR]

The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket. [ABSTRACT FROM AUTHOR]

The transcription factor TRANSPARENT TESTA 16 ( TT16) plays an important role in endothelial cell specification and proanthocyanidin ( PA) accumulation. However, its precise regulatory function with regard to the expression of endothelial-associated genes in developing seeds, and especially in the PA-producing inner integument, remains largely unknown. Therefore, we endeavored to characterize four TT16 homologs from the allotetraploid oil crop species Brassica napus, and systematically explore their regulatory function in endothelial development. Our results indicated that all four BnTT16 genes were predominantly expressed in the early stages of seed development, but at distinct levels, and encoded functional proteins. Bntt16 RNA interference lines exhibited abnormal endothelial development and decreased PA content, while PA polymerization was not affected. In addition to the previously reported function of TT16 in the transcriptional regulation of anthocyanidin reductase ( ANR) and dihydroflavonol reductase ( TT3), we also determined that BnTT16 proteins played a significant role in the transcriptional regulation of five other genes involved in the PA biosynthetic pathway ( P < 0.01). Moreover, we identified two genes involved in inner integument development that were strongly regulated by the BnTT16 proteins ( TT2 and δ-vacuolar processing enzyme). These results will better our understanding of the precise role of TT16 in endothelial development in Brassicaceae species, and could potentially be used for the future improvement of oilseed crops. [ABSTRACT FROM AUTHOR]

Abstract: Fourfold paralogy regions in the human genome have been considered historical remnants of whole-genome duplication events predicted to have occurred early in vertebrate evolution. Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the prediction that the ancestral vertebrate genome was shaped by two rapid rounds of whole-genome duplication within a period of 10 million years. Both the map self-comparison approach and a phylogenetic analysis revealed that gene families identified as tetralogous on human chromosomes 1/2/8/20 arose by small-scale duplication events that occurred at widely different time points in animal evolution. Furthermore, the data discount the likelihood that tree topologies of the form ((A,B)(C,D)) are best explained by the octoploidy hypothesis. We instead propose that such symmetrical tree patterns are also consistent with local duplications and rearrangement events. [Copyright &y& Elsevier]

Abstract: Acetyl-CoA short chain synthetases (ACSSs) are key enzymes in the activation of fatty acids through the formation of thioesters with CoA. Three subfamily members are currently recognized in the human genome, ACSS1, ACSS2 and ACSS3, all single copy genes. The mitochondrial isoform, Acss1, plays a key role in the metabolism of acetate for energy production. While the single copy condition has been accurately established in humans, the evolutionary history of the Acss1 subfamily in vertebrates has yet to be elucidated, in particular, the isoform diversity, origin and function. Through genome database mining we analyzed the diversity of Acss1 isoforms in vertebrate classes. We detected the presence of a novel Acss1 isoform, which we name Acss1B. This new gene, Acss1B, has a curious phylogenetic distribution being found in teleosts (except zebrafish), sauropsids (birds and reptiles) and probably chondrichthyes. In contrast Acss1A is found in all the investigated species, except the teleost medaka. By means of comparative genomics and phylogenetics we show that Acss1A and Acss1B were generated in the quadruplication of the vertebrate genome. In effect, we find that amphioxus, a pre-genome duplication chordate, has a single Acss1 gene in a genomic region equally related to a quadrupled vertebrate genomic set. Consequently, Acss1B has been lost in some teleosts, amphibians and mammals, while Acss1A is probably absent in medaka. The reported findings illustrate an especially dynamic pattern of paralogue retention and independent loss in vertebrate species involving the Acss1 subfamily, whose functional consequences in energy metabolism are as yet unknown. [Copyright &y& Elsevier]

Current data on the Y-specific sex-determining region of salmonid fishes from genera Salvelinus, Salmo, and Oncorhynchus indicate variable polymorphisms in the homologous chromosomal locations of the sex-specific determining region. In the majority of the Atlantic lineage Arctic charr, including populations from the Fraser River, in Labrador Canada, as well as Swedish and Norwegian strains, the sex-determining locus maps to linkage group AC-4. Previously, sex-linked polymorphisms (i.e., variation in the associated sex-linked markers on AC-4) have been described in Arctic charr. Here, we report further evidence for intraspecific sex linkage group polymorphisms in Arctic charr (i.e., the detection of the SEX locus on either the AC-1 or AC-21 linkage group) and a possible conservation of a sex linkage arrangement in Icelandic Arctic charr and Atlantic salmon, involving sex-linked markers on the AC-1/21 homeologs and the European AS-1/6 homeologous linkage groups in Atlantic salmon. The evolutionary origins for the multiple sex-determining regions within the salmonid family are discussed. We also relate the variable sex-determining regions in salmonids to their ancestral proto-teleost karyotypic origins and compare these findings with what has been observed in other teleost species in general. [ABSTRACT FROM AUTHOR]

Abstract: The social amoeba Dictyostelium discoideum contains only one aromatic amino acid hydroxylase (AAAH) gene compared to at least three in metazoans. As shown in this work this gene codes for a phenylalanine hydroxylase (DictyoPAH) and phylogenetic analysis places this enzyme close to the precursor AAAHs, aiding to define the evolutionary history of the AAAH family. DictyoPAH shows significant similarities to other eukaryote PAH, but it exhibits higher activity with tetrahydrodictyopterin (DH4) than with tetrahydrobiopterin (BH4) as cofactor. DH4 is an abundant tetrahydropterin in D. discoideum while BH4 is the natural cofactor of the AAAHs in mammals. Moreover, DictyoPAH is devoid of the characteristic regulatory mechanisms of mammalian PAH such as positive cooperativity for L-Phe and activation by preincubation with the substrate. Analysis of the few active site substitutions between DictyoPAH and mammalian PAH, including mutant expression analysis, reveals potential structural determinants for allosteric regulation. [Copyright &y& Elsevier]

The mammalian proglucagon gene encodes three related sequences, glucagon and the glucagon-like peptides 1 and 2 (GLP-1 and GLP-2), each of which has an essential role in metabolism. A family of closely related receptors mediates the physiological actions of these hormones. Intriguingly, GLP-1 has opposite functions in mammals and fish. In mammals, secretion of GLP-1 results in a reduction in blood sugar levels, whereas in fish it causes an increase. The recent release of draft genome sequences of diverse vertebrates has made it possible to examine the evolution of the receptors for these peptide hormones. Phylogenetic analysis of sequences of receptors for proglucagon-encoded hormones suggests a potential explanation for the change in function of GLP-1 between fish and mammals. I suggest that in fish, GLP-l lost the ability to act on insulin-secreting cells and was recruited as a ligand for a duplicated glucagon receptor, resulting in a physiological action similar to that of glucagon. [ABSTRACT FROM AUTHOR]

The melanocortin receptors (MCR) belong to the superfamily of G-protein-coupled receptors that participate in both peripheral and central functions, including regulation of energy balance. Genomic clones of the five chicken (GGA) MCRs were isolated and used to find the chromosomal location of each of the loci. The genes encoding MC2R and MC5R mapped to the middle part of the long arm of chromosome 2 (GGA2q22–q26) and MC4R proximally on the same chromosome arm, close to the centromere (2q12). This arrangement seems to be conserved on chromosome 18 in the human (HSA18). The MC1R and MC3R genes mapped to different microchromosomes that also appear to share homology with the respective human localization. The conserved synteny of the MC2R, MC5R, and MC4R cluster in chicken (GGA2), human (HSA18), and other mammals suggests that this cluster is ancient and was formed by local gene duplications that most likely occurred early in vertebrate evolution. Analysis of conserved synteny with mammalian genomes and paralogon segments prompted us to predict an ancestral gene organization that may explain how this family was formed through both local duplication and tetraploidization processes. [Copyright &y& Elsevier]

All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.

The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket., (© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)