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Background and aims: Over-grazing have significantly altered above- and belowground functions in terrestrial ecosystem. However, the influence of grazing intensity on plant-soil stoichiometric relations in alpine ecosystems remains unclear. Methods: We investigated the responses of plant-soil nutrient stoichiometric relationships to four grazing intensities (un-grazing (UG), light grazing (LG), moderate grazing (MG) and heavy grazing (HG)) in an alpine meadow on the eastern Tibetan Plateau. We measured carbon (C), nitrogen (N), phosphorus (P) and potassium (K) concentrations and their ratios in plants and soils in the peak growing season after three years of yak-grazing. Results: Compared to UG and LG plots, heavier grazing intensity at community levels and taxonomic groups decreased plant C and K concentrations by 7.6–10.5% and 17.6–21.3%, respectively, while grazing did not significantly influence plant N and P concentrations. Grazing intensity altered plant C:N and C:P ratios but not C:K and N:P ratios. By contrast, grazing intensity had no significant effects on soil nutrients and stoichiometry. Thus, the differential responses of plant and soil nutrients to grazing intensity caused that plants were more sensitive to grazing than soils. Conclusions: Our results confirm that grazing intensity has differential effects on plant and soil nutrients, implying that plant nutrients do not covary with soil nutrients under changing grazing intensity and challenging the past positive relations between plant and soil nutrients. Further long-term grazing experiments are required to understand the drivers of grazing effect on plant-soil nutrient interactions. [ABSTRACT FROM AUTHOR]

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants. A chromosome-level genome assembly for the glasshouse plant Rheum nobile (noble rhubarb) combined with phylogenetic, transcriptomic, and metabolomic analyses provides insight into how alpine plants have adapted to growth in extreme environments. [ABSTRACT FROM AUTHOR]

Introgression frequently occurs between closely related plant species when there is incomplete reproductive isolation. However, few studies have been designed to examine the extent and direction of introgression from all three genomes, especially when they have different rates of gene flow. Conifers, in which chloroplast (cp), mitochondrial (mt) and nuclear (nr) genomes show contrasting rates of gene flow, provide a good model in which to carry out such a case study. Here we use data on sequence variation in 18 DNAs from three genomes for 311 individuals of 31 populations to investigate the extent and direction of introgressions between three spruce species in areas where they are sympatrically distributed. We found that one species seem to have introgressions derived from the other two species in areas of sympatric distribution; there were more introgressions from the maternally inherited mtDNA, which has the lowest rate of gene flow, and fewer introgressions from the bi-parentally inherited nrDNA. Further coalescent analysis of nrDNA population genetic data suggested that the species containing introgressions had experienced range expansion in the recent past while there was no such indication for the other two species. Our results support the hypotheses that introgressions occurred more frequently at genetic markers with lower rates of gene flow and that they usually took place from local species towards invading species that had undergone recent demographic expansion. [ABSTRACT FROM AUTHOR]

Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis, although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis- P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands. [ABSTRACT FROM AUTHOR]

Polyploidization has contributed greatly to current plant diversity. Allopolyploid speciation, which can rapidly overcome meiosis abnormalities, is a common and repeated process in numerous genera. However, most polyploids within a single morphological/taxonomic species have been considered autopolyploids, which were assumed to arise through spontaneous genome doubling and/or following the fusion of unreduced diploid gametes. It remains untested whether these intraspecific polyploids may also be the result of 'allopolyploid' hybridizations between differentiated diploid populations and whether such speciation has also occurred repeatedly. In this study, we examined the diploid-tetraploid species Allium przewalskianum on the Qinghai-Tibet Plateau (QTP) to test this cryptic speciation hypothesis under morphological stasis, based on three sets of nuclear genetic data (AFLP, ITS, and CHS) and niche modeling. Our analyses of the three datasets together revealed that the diploid populations across the northeastern to southeastern QTP exhibit strong geographical differentiation. Based on the shared nuclear lineages fixed in the different diploids, three tetraploid groups in the northern, southern, and eastern QTP were identified as having originated independently, through 'allopolyploid' hybridization between the differentiated diploids. Ecological niche modeling based on ecological variables suggested distinct niche differentiation between two tetraploid groups in the northern and southern QTP and also between these and the diploid populations. Furthermore, they also differed in their responses to past climate changes. These findings together suggested that at least two tetraploid groups had originated independently through hybridizations between the differentiated diploid populations. Our results highlight the cryptic allopolyploid speciation underlying a single morphological species, which mirrors well the repeated allopolyploid speciations within the genus. This allopolyploid speciation may prevail within the diploid-polyploid species complex that is classified as a single morphological species; indeed, the underlying cryptic speciation and evolutionary dynamics are certainly more complex than previously assumed. [ABSTRACT FROM AUTHOR]

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient introgression from a cypress species (Cupressus gigantea) that occurs at higher latitude and elevation on the Qinghai-Tibet Plateau into a related species (C. duclouxiana), which has likely aided the latter species to extend its range by colonizing cooler and drier mountain habitats during postglacial periods. We show that 16 introgressed candidate adaptive loci could have played pivotal roles in response to diverse stresses experienced in a high-elevation environment. Our findings provide new insights into the evolutionary history of Qinghai-Tibet Plateau plants and the importance of introgression in the adaptation of species to climate change. Yazhen Ma et al. find evidence of an ancient introgression from cypress into a related species from the Qinghai-Tibet Plateau, which aided in the colonization of cooler and drier mountain habitats. They identify 16 introgressed loci that may provide protection against high-elevation stressors. [ABSTRACT FROM AUTHOR]

Wood, which consists mainly of plant cell walls, is an extremely important resource in daily lives. Genes whose products participate in the processes of cell wall and wood formation are therefore major subjects of plant science research. The Wood-Formation Related Genes database (WFRGdb, http://me.lzu.edu.cn/woodformation/) serves as a data resource center for genes involved in wood formation. To create this database, we collected plant genome data published in other online databases and predicted all cell wall and wood formation related genes using BLAST and HMMER. To date, 47 gene families and 33 transcription factors from 57 genomes (28 herbaceous, 22 woody and 7 non-vascular plants) have been covered and more than 122,000 genes have been checked and recorded. To provide easy access to these data, we have developed several search methods, which make it easy to download targeted genes or groups of genes free of charge in FASTA format. Sequence and phylogenetic analyses are also available online. WFRGdb brings together cell wall and wood formation related genes from all available plant genomes, and provides an integrative platform for gene inquiry, downloading and analysis. This database will therefore be extremely useful for those who focuses on cell wall and wood research. [ABSTRACT FROM AUTHOR]