Suchergebnisse

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary. Copyright: © 2014 Bischoff et al. ; Financial support for this study was provided by a Fundación BBVA BIOCON 05-093/06 project grant to PC and JGSM. JV was supported by a Fundación BBVA Ph.D. grant. JGSM was supported by two consecutive Spanish Aragón Government ''Araid'' and Spanish Ministry of Science and Innovation ''Ramón y Cajal'' postdoctoral contracts. PC was partially funded by a Bioflora (http://bifi.es/bioflora/) research team grant co-funded by the Spanish Aragón Government and the European Social Fund. ; Peer Reviewed

Recent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero-Proven̤al belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub-structured into two geographically separated subgroups (SE+E Iberia and NE Iberia+SW France). Genetic diversity and spatial structure analyses suggested a mid-Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle-Late Pleistocene marine regressions, whereas the more recent single back-colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long-distance dispersal mediated by migratory marine birds or sea currents. ; This work was supported by MICINN РSpanish Government grant projects (CGL2007-64839-C02-01,CGL2010-22234-C02-01 and 200630I241 Intramural), the SGR (2009SGR439) Generalitat de Catalunya project and the Aragon Government Bioflora project, cofunded by the European FEDER programme ; Peer Reviewed

Plant survival in alpine habitats is controlled, in several cases, by pollination and seed dispersal success. We have investigated the genetic structure and mating patterns of the endangered Borderea pyrenaica (Dioscoreaceae), one of the oldest herbaceous Pyrenean mountain plants. Simple sequence repeat-based genotyping was carried out on all the reproductive female and male individuals and in all the female-descendent progenies of a population of this plant. Although the offspring sampling (246) was twice the size of the adult sampling (122), the latter group showed higher levels of heterozygosity and approximately 20% more alleles than the offspring. Probabilistic spatial neighbourhood modelling of parentage analysis, based on the exponential-power type model, showed immigration rates of pollen at 63.3%. The present study also detected a strong spatial clustering; most of the sired seeds of B. pyrenaica (68.83%) occurred at distances of up to 20 m, whereas kinship coefficients of adult plants reached zero at spatial distances (d) < 5 m, and 5 < d < 10 m for females and males, respectively. These results support the hypothesis of a terrestrial ant-mediated, rather than a flying insect-mediated pollination in B. pyrenaica. © 2015 The Linnean Society of London. ; We thank Juan José Robledo-Arnuncio and two anonymous reviewers for their valuable comments and for critically reviewing an earlier version of the manuscript, as well as Emily Lemonds and Douglas Laing for linguistic assistance. The present study has been funded by a Fundación BBVA project grant BIOCON05/093. E. Pérez-Collazos was supported by a Postdoctoral grant from the Fundación BBVA. J. G. Segarra-Moragues was funded by two consecutive Spanish Aragón Government 'Araid' and Spanish Ministry of Science and Innovation 'Ramón y Cajal' postdoctoral contracts, respectively. The work was partially supported by a Bioflora research group grant, co-funded by the Aragón Government and the European Social Fund. ; Peer Reviewed

18 Pags.- 1 Tabl.- 7 Figs. © 2020 The Authors. Under Creative Commons License Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). ; Globins (Glbs) are widely distributed in archaea, bacteria and eukaryotes. They can be classifiedinto proteins with 2/2 or 3/3 a-helical folding around the heme cavity. Both types of Glbs occur ingreen algae, bryophytes and vascular plants. The Glbs of angiosperms have been moreintensively studied, and several protein structures have been solved. They can be hexacoordinateor pentacoordinate, depending on whether a histidine is coordinating or not at the sixth positionof the iron atom. The 3/3 Glbs of class 1 and the 2/2 Glbs (also called class 3 in plants) are presentin all angiosperms, whereas the 3/3 Glbs of class 2 have been only found in early angiospermsand eudicots. The three Glb classes are expected to play different roles. Class 1 Glbs are involvedin hypoxia responses and modulate NO concentration, which may explain their roles in plantmorphogenesis, hormone signaling, cell fate determination, nutrient deficiency, nitrogenmetabolism and plant–microorganism symbioses. Symbiotic Glbs derive from class 1 or class 2Glbs and transport O2in nodules. The physiological roles of class 2 and class 3 Glbs are poorlydefined but could involve O2and NO transport and/or metabolism, respectively. More researchis warranted on these intriguing proteins to determine their non-redundant functions. ; Part of the work described in the lab of MB wasfunded by the Spanish Ministry of Science and Innovation-European Regional Development Fund (grant AGL2017-85775-R) and by Government of Aragón, Spain (group A09_17R). ; Peer reviewed

Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species. ; Financial support was provided by the Spanish projects PI097/08 from the Aragón Government, GA-LC-012/2008 from the Aragón Government-La Caixa, 059/2009 from the Ministry of Environment (National Parks division) and a European Union ESF exchange grant (FroSpects 3142). IM received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement PIOF-GA-2011-301257. DD was supported by the Portuguese Foundation for Science and Technology (SFRH/BPD/100384/2014). IM, MLLH and PC benefitted from the Bioflora grant project cofunded by the Aragón government and the European Social Fund. JGS-M was supported by two consecutive Aragón Government "Araid" and the Spanish Ministry of Science and Innovation "Ramón y Cajal" postdoctoral contracts. ; Peer reviewed

[Background and Aims] It is accepted that contemporary allopolyploid species have originated recurrently, but very few cases have been documented using multiple natural formations of the same species. To extend our knowledge, we have investigated the multiple origins, genetic variation and structure of the allotetraploid grass Brachypodium hybridum with respect to its progenitor diploid species B. distachyon (D genome) and B. stacei (S genome). For this, our primary focus is the Iberian Peninsula, an evolutionary hotspot for the genus Brachypodium. ; [Methods] We analysed 342 B. hybridum individuals from 36 populations using ten nuclear SSR loci and two plastid loci. The B. hybridum genetic profiles were compared with those previously reported for B. stacei and B. distachyon. In addition, phylogenetic analysis of the plastid data was performed for a reduced subset of individuals. ; [Key Results] The nuclear simple sequence repeat (SSR) genetic analysis detected medium to high genetic diversity, with a strong south-to-north genetic structure cline, and a high selfing rate in B. hybridum. Comparative genetic analysis showed a close relatedness of current B. hybridum D allelic profiles with those of B. distachyon, but a lack of similarity with those of B. stacei, suggesting another B. stacei source for the B. hybridum S alleles. Plastid analysis detected three different bidirectional allopolyploidization events: two involved distinct B. distachyon-like ancestors and one involved a B. stacei-like ancestor. The south-eastern Iberian Peninsula B. hybridum populations were more genetically diverse and could have originated from at least two hybridization events whereas north-eastern/north-western Iberian Peninsula B. hybridum populations were less diverse and may have derived from at least one hybridization event. ; [Conclusions] The genetic and evolutionary evidence supports the plausible in situ origin of the south-eastern and northern Iberian Peninsula B. hybridum allopolyploids from their respective local B. distachyon and unknown B. stacei ancestors. The untapped multiple origins and genetic variation detected in these B. hybridum populations opens the way to future evolutionary analysis of allopolyploid formation and genomic dominance and expression in the B. hybridum–B. distachyon–B. stacei grass model complex. ; This work was supported by the Spanish Ministry of Economy and Competitivity (Mineco) CGL2016-79790-P and University of Zaragoza UZ2016_TEC02 grant projects. V.S. was funded by a Russian Ministry of Science and Higher Education fellowship and grant RFBR no. 18-34-00901. P.C. and I.M. were partially funded by a European Social Fund and Aragón Government Bioflora grant.

[Background] Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas. ; [Results] We found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula. ; [Conclusions] The finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals. ; The study has been funded by two consecutive Spanish Ministry of Economy and Competitiveness grant projects (CGL2012–39953-C02–01, CGL2016–79790-P) and one Aragon Government and European Social Fund Bioflora grant to PC and IM. DL-A and VS were funded by a Spanish Ministry of Science and Innovation and a Tomsk State University PhD fellowship, respectively. DL-A was also supported by a Spanish Instituto de Estudios Altoaragoneses grant. IM received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement PIOF-GA-2011-301,257. PH was funded by Spanish Junta de Andalucia project AGR-0482. ; Peer reviewed

99 pags.- Tabls.- Figs. This is the pre-peer reviewed version of the article doi 10.1111/nph.14926 which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/nph.14926/abstract This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. ; Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure. ; P.C., B.C-M., R.S. and D.L-A. received funding from the Spanish Ministry of Economy and Competitivity (Mineco) grant projects (CGL2012-39953-C02-01, CSIC13-4E-2490 and CGL2016-79790-P). B.C-M. was funded by Fundación ARAID. R.S. and D.L-A. were funded by their respective Spanish Mineco PhD fellowships. P.C., R.S. and D.L-A. were partially funded by a Bioflora grant cofunded by the Spanish Aragon Government and the European Social Fund. The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. ; Peer reviewed

29 Pags.- 6 Figs. © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. ; Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus' flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses. ; This research was funded by Spanish Ministry of Science and Innovation grant number PID2019-108195GB-I00, European Social Fund/Spanish Aragón Government grant number A01-20R, Spanish Junta de Andalucía grant number P18-RT-992, USDA grant number NIFA-2011-67012- 30663. MD was funded by a Spanish Mineco FPI PhD fellowship. BCM was funded by Spanish Fundación ARAID. ; Peer reviewed

13 Pags.- 6 Figs. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder ; While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution. ; The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. D.P. W. and R.A. were funded in part by the National Science Foundation (grant no. IOS–1258126), and the Great Lakes Bioenergy Research Center (Department of Energy Biological and Environmental Research Office of Science grant no. DE– FCO2–07ER64494). TEJ and DLDM were supported by NSF PGRP grant IOS-0922457. P.C. and B.C.M. were funded by Spanish MINECO (CGL2012-39953-C02-01 and CGL2016-79790-P). B.C.M. was partially funded by DGA—Obra Social La Caixa (grant number GA-LC-059-2011) and Spanish MINECO (AGL2013-48756-R, CSIC13-4E-2490). PC was partially funded by Spanish Aragon Government-European Social Fund (Bioflora). ; Peer reviewed

16 Pags.- 8 Figs. This article is licensed under a Creative Commons Attribution 4.0 International License. ; Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution. ; The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231 and User Agreement No. FP00006675 between the University of Zaragoza (User) and the DOE (Community Science Program 503504 proposal); S.J. was supported by the DOE Office of Science Graduate Student Research Program; P.C., B.C.-M., A.D.P., and R.S. were supported by a Spanish Ministry of Economy and Competitiveness grant CGL2016-79790-P; P.C., A.D.P., and R.S. were supported by a Bioflora A01-17 grant co-funded by the Spanish Aragon Government and the European Social Fund. R.H., E.W., and J.L. were supported by the National Science Centre Poland (grants DEC-2012/04/A/NZ3/00572 and DEC-2014/14/M/NZ2/00519). J.H.D. and C.N. were supported by Leverhulme Trust (grant no. 10754). A.C.E. and A.D. were supported by the European Research Council under the European Union's Seventh Framework Program (FP7/2007-2013)/ERC grant agreement no [GA335691 "Effectomics"], the Austrian Science Fund (FWF): [P27429-B22, P27818-B22, I 3033-B22], and the Austrian Academy of Science (OEAW). ; Peer reviewed