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Keywords: Buddleja (Scrophulariaceae); hybridization; polyploidization EN Buddleja (Scrophulariaceae) hybridization polyploidization v vii 1 10/06/23 20230701 NES 230701 Reticulate evolution involves hybrid speciation events that combine two species to produce a third one with or without polyploidization, introgression and horizontal gene transfer between different species (Fig. Their results further show that the Quaternary climatic oscillations, which possibly led to range changes following hybridizations between previously isolated species, have greatly contributed to a pattern of species diversification through both allopatric and (sympatric) hybrid speciation (Fig. The high proportion of polyploid species obviously suggests that polyploidization should have contributed greatly to the species diversification of this genus in the Sino-Himalayan region, in contrast to the early predication that the species diversification in this region mainly occurs at the diploid level ([10]). Hybridization and polyploidization generate evolutionary diversification of the genus Buddleja in the Sino-Himalayan region. [Extracted from the article]

Long noncoding ribonucleic acids (lncRNAs) play crucial roles in regulating key biological processes; however, our knowledge of lncRNAs' roles in plant adaptive evolution is still limited. Here, we determined the divergence of conserved lncRNAs in closely related poplar species that were either tolerant or sensitive to salt stress by comparative transcriptome analysis. Among the 34,363 identified lncRNAs, ~3% were shared among poplar species with conserved sequences but diversified in their function, copy number, originating genomic region and expression patterns. Further cluster analysis revealed that the conserved lncRNAs showed more similar expression patterns within salt-tolerant poplars (Populus euphratica and P. pruinosa) than between salt-tolerant and salt-sensitive poplars. Among these lncRNAs, the antisense lncRNA lncERF024 was induced by salt and the differentiated expression between salt-sensitive and salt-tolerant poplars. The overexpression of lncERF024 in P. alba var. pyramidalis enhanced poplar tolerance to salt stress. Furthermore, RNA pull-down and RNA-seq analysis showed that numerous candidate genes or proteins associated with stress response and photosynthesis might be involved in salt resistance in PeulncERF024-OE poplars. Altogether, our study provided a novel insight into how the diversification of lncRNA expression contributes to plant adaptation traits and showed that lncERF024 may be involved in the regulation of both gene expression and protein function conferring salt tolerance in Populus. [ABSTRACT FROM AUTHOR]

Background and Aims Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis – Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. Methods A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. Key Results Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. Conclusions Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies. [ABSTRACT FROM AUTHOR]

Oxygen deprivation caused by flooding activates acclimation responses to stress and restricts plant growth. After experiencing flooding stress, plants must restore normal growth; however, which genes are dynamically and precisely controlled by flooding stress remains largely unknown. Here, we show that the Arabidopsis thaliana ubiquitin E3 ligase SUBMERGENCE RESISTANT1 (SR1) regulates the stability of the transcription factor WRKY33 to modulate the submergence response. SR1 physically interacts with WRKY33 in vivo and in vitro and controls its ubiquitination and proteasomal degradation. Both the sr1 mutant and WRKY33 overexpressors exhibited enhanced submergence tolerance and enhanced expression of hypoxia-responsive genes. Genetic experiments showed that WRKY33 functions downstream of SR1 during the submergence response. Submergence induced the phosphorylation of WRKY33, which enhanced the activation of RAP2.2 , a positive regulator of hypoxia-response genes. Phosphorylated WRKY33 and RAP2.2 were degraded by SR1 and the N-degron pathway during reoxygenation, respectively. Taken together, our findings reveal that the on-and-off module SR1-WRKY33- RAP2.2 is connected to the well-known N-degron pathway to regulate acclimation to submergence in Arabidopsis. These two different but related modulation cascades precisely balance submergence acclimation with normal plant growth. [ABSTRACT FROM AUTHOR]

Salinity restricts the growth of trees to varying extents, but the regulatory mechanisms involved in their varying salt tolerance are largely unknown. In an effort to elucidate these mechanisms, we identified a total of 99 genes in the Ethylene Responsive Factor (ERF) family of transcription factors and examined their expression patterns under salt stress in Populus alba var. pyramidalis. We found that a B4 group gene, PalERF109 , was rapidly induced by salt treatment and preferentially expressed in stems and petioles, where it is probably involved in transport of ions and water in xylem. Overexpression of PalERF109 enhanced the salt tolerance of the poplar, and further analysis showed that it directly upregulated a high-affinity K + transporter (HKT) gene, PalHKT1;2. The results clearly indicate that PalERF109 enhances salt tolerance at least partially through direct activation of PalHKT1;2 and extends understanding of the roles of ERF genes in tree stress responses. [ABSTRACT FROM AUTHOR]

Background and Aims Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in conifers concerns generic relationships within the subfamily Cupressoideae (105 species, approx. 1/6 of all conifers) of Cupressaceae, in particular the relationship between Juniperus, Cupressus and the Hesperocyparis – Callitropsis – Xanthocyparis (HCX) clade. Here we attempt to resolve this question using transcriptome-derived data. Methods Transcriptome sequences of 20 species from Cupressoideae were collected. Using MarkerMiner, single-copy nuclear (SCN) genes were extracted. These were applied to estimate phylogenies based on concatenated data, species trees and a phylogenetic network. We further examined the effect of alternative backbone topologies on downstream analyses, including biogeographic inference and dating analysis. Results Based on the 73 SCN genes (>200 000 bp total alignment length) we considered, all tree-building methods lent strong support for the relationship (HCX, (Juniperus, Cupressus)); however, strongly supported conflicts among individual gene trees were also detected. Molecular dating suggests that these three lineages shared a most recent common ancestor approx. 60 million years ago (Mya), and that Juniperus and Cupressus diverged about 56 Mya. Ancestral area reconstructions (AARs) suggest an Asian origin for the entire clade, with subsequent dispersal to North America, Europe and Africa. Conclusions Our analysis of SCN genes resolves a controversial phylogenetic relationship in the Cupressoideae, a major clade of conifers, and suggests that rapid evolutionary divergence and incomplete lineage sorting probably acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Our updated backbone topology has not substantially altered molecular dating estimates relative to previous studies; however, application of the latest AAR approaches has yielded a clearer picture of the biogeographic history of Cupressoideae. [ABSTRACT FROM AUTHOR]

The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Evidence of genetic exchange between diverging taxa is reported frequently, although most studies fail to show how hybridization and introgression contribute to the adaptation and differentiation of introgressed taxa. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex, which comprises four taxa occurring in the biodiversity hotspot of the Hengduan–Himalayan mountains. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree‐like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA–BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa. [ABSTRACT FROM AUTHOR]

Background and Aims Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance. Methods Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome. Key Results In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor–derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence. Conclusions The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species. [ABSTRACT FROM AUTHOR]

Population genetics data based on multiple nuclear loci provide invaluable information to understand demographic, selective, and divergence histories of the current species. We studied nucleotide variation at 13 nuclear loci in 53 populations distributed among four closely related, but morphologically distinct juniper species of the Qinghai-Tibetan Plateau (QTP). We used a novel approach combining Approximate Bayesian Computation and a recently developed neutrality test based on the maximum frequency of derived mutations to examine the demographic and selective histories of individual species, and isolation-with-migration analyses to study the joint history of the species and detect gene flow between them. We found that (1) the four species, which diverged in response to the extensive QTP uplifts, have different demographic histories; (2) two loci, Pgi and CC0822, depart significantly from neutrality in one species and Pgi, is also marginally significant in another; and (3) shared polymorphisms are common, indicating both incomplete lineage sorting and gene flow after species divergence. In addition, the detected unidirectional gene flow provides indirect support for the theoretical prediction that introgression should mostly take place from local to invading species. Our results, together with previous studies, underscore complex evolutionary histories of plant diversification in the biodiversity-hotspot QTP. [ABSTRACT FROM AUTHOR]

Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species. [ABSTRACT FROM AUTHOR]