Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests.

Current global climate change is expected to affect biodiversity negatively at all scales leading to mass biodiversity loss. Many studies have shown that the distribution of allele frequencies across a species' range is often influenced by specific genetic loci associated with local environmental variables. This association reflects local adaptation and allele changes at those loci could thereby contribute to the evolutionary response to climate change. However, predicting how species will adapt to climate change from this type of data alone remains challenging. In the present study, we combined exome capture sequences and environmental niche reconstruction, to test multiple methods for assessing local adaptation and climate resilience in two widely distributed conifers, Norway spruce and Siberian spruce. Both species are keystone species of the boreal forest and share a vast hybrid zone. We show that local adaptation in conifers can be detected through allele frequency variation, population-level ecological preferences, and historical niche movement. Moreover, we integrated genetic and ecological information into genetic offset predictive models to show that hybridization plays a central role in expanding the niche breadth of the two conifer species and may help both species to cope better with future changing climates. This joint genetic and ecological analysis also identified spruce populations that are at risk under current climate change.

A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection.

Recent studies have highlighted the significant role of copy number variants (CNVs) in phenotypic diversity, environmental adaptation and species divergence across eukaryotes. The presence of CNVs also has the potential to introduce genotyping biases, which can pose challenges to accurate population and quantitative genetic analyses. However, detecting CNVs in genomes, particularly in non-model organisms, presents a formidable challenge. To address this issue, we have developed a statistical framework and an accompanying r software package that leverage allelic-read depth from single nucleotide polymorphism (SNP) data for accurate CNV detection. Our framework capitalises on two key principles. First, it exploits the distribution of allelic-read depth ratios in heterozygotes for individual SNPs by comparing it against an expected distribution based on binomial sampling. Second, it identifies SNPs exhibiting an apparent excess of heterozygotes under Hardy-Weinberg equilibrium. By employing multiple statistical tests, our method not only enhances sensitivity to sampling effects but also effectively addresses reference biases, resulting in optimised SNP classification. Our framework is compatible with various NGS technologies (e.g. RADseq, Exome-capture). This versatility enables CNV calling from genomes of diverse complexities. To streamline the analysis process, we have implemented our framework in the user-friendly r package 'rCNV', which automates the entire workflow seamlessly. We trained our models using simulated data and validated their performance on four datasets derived from different sequencing technologies, including RADseq (Chinook salmon-Oncorhynchus tshawytscha), Rapture (American lobster-Homarus americanus), Exome-capture (Norway spruce-Picea abies) and WGS (Malaria mosquito-Anopheles gambiae).

Out of chaos: Phylogenomics of Asian Sonerileae.

Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.

Rosuvastatin corrects oxidative stress and inflammation induced by LPS to attenuate cardiac injury by inhibiting the NLRP3/TLR4 pathway.

Rosuvastatin has been found to possess antioxidant and anti-inflammatory properties. The aim of the current study was to evaluate whether rosuvastatin was effective in attenuating cardiac injury in lipopolysaccharide (LPS) - challenged mice and H9C2 cells and identify the underlying mechanisms, focusing on the nod-like receptor protein 3 (NLRP3)/toll-like receptor 4 (TLR4) pathway. Cardiac injury, cardiac function, apoptosis, oxidative stress, inflammatory response, and the NLRP3/TLR4 pathway were evaluated in both in vivo and in vitro studies. LPS-induced cardiomyocyte injury was markedly attenuated by rosuvastatin treatment, evidenced by increased cell proliferation of H9C2 cells, rescued cardiac function, and improved morphological changes in mice and reduced lactate dehydrogenase (LDH), creatine kinase MB fraction (CK-MB), and troponin I (cTnI) in serum. Apoptosis was clearly ameliorated in myocardial tissue and H9C2 cells co-treated with rosuvastatin. In addition, after LPS challenge, excessive oxidative stress was present, indicated by increases in malondialdehyde (MDA) content, NADPH activity, and reactive oxygen species (ROS) production and decreased superoxide dismutase (SOD) activity. Rosuvastatin improved all the indicators of oxidative stress, with an effect similar to that of N-acetylcysteine (NAC) (an ROS scavenger). Notably, LPS-exposed H9C2 cells and mice showed significant NLRP3 and TLR4/nuclear factor-κB (NF-κB) pathway activation and inflammatory responses. Administration of rosuvastatin reduced the increases in NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), pro-caspase-1, TLR4, and p65 expression and decreased the tumor necrosis factor α (TNF-α), interleukin 1ß (IL-1ß), IL-18, and IL-6 contents, with an effect similar to that of MCC950 (an NLRP3 inhibitor). In conclusion, inhibition of the inflammatory response and oxidative stress contributes to cardioprotective effect of rosuvastatin against cardiac injury induced by LPS, and the effect of rosuvastatin was achieved through inactivation of the NF-κB/NLRP3 pathway.

A new species of Bredia (Sonerileae, Melastomataceae) from Sichuan, China.

Bredia hispida (Sonerileae, Melastomataceae), a species occurring in southeastern Sichuan, China, is newly described based on morphological and molecular data. The generic placement of B. hispida is well supported by phylogenetic analysis and morphological characters, including basally cordate, hairy leaf blade, cymose inflorescence, basally gibbous anthers and enlarged ovary crown enclosing an inverted frustum-shaped depression. Both molecular and morphological divergence showed that B. hispida is well separated from its close relatives, justifying its recognition as a distinct species. The new species resembles B. repens, B. changii and B. guidongensis in the prostrate habit and isomorphic stamens but differs markedly in the unequal opposed leaves, the 2-4 mm long, stout bristles on the adaxial surface of leaf blade and acuminate leaf apex. Bredia hispida co-occurs with B. esquirolii in the wild. No morphologically putative hybrids between them were observed despite their overlap in flowering season. The isolating mechanism remains unclear, pending further investigation.

Natural hybridization between Phyllagathis and Sporoxeia species produces a hybrid without reproductive organs.

Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.

Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae.

Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.

Recircumscription of Bredia and resurrection of Tashiroea (Sonerileae, Melastomataceae) with description of a new species T.villosa.

Bredia (Melastomataceae) is an Asian genus that extends from central and southern mainland China to Taiwan and the Ryukyu islands. Molecular phylogenetic analyses reveal that the type of Bredia is nested in a clade of 20 species, while Tashiroea, a genus previously synonymized in Bredia, falls in another distantly related clade of 10 species. Our morphological survey shows that the two clades can be distinguished by several diagnostic features including leaf indumentum, texture, leaf surface sculpture under SEM, presence/absence of yellowish uniseriate trichomes, and capsule morphology. Based on molecular and morphological evidence, Bredia is recircumscribed and Tashiroea is resurrected. Description and a list of species are provided for the two genera with the description of a new species, T.villosa.

A new species of Fordiophyton (Sonerileae, Melastomataceae) from Yunnan, China.

Fordiophytonjinpingense (Melastomataceae; Sonerileae), a species occurring in south-eastern Yunnan, China, is described as new, based on morphological and molecular data. Phylogenetic analyses, based on nrITS sequence data, showed that, except F.breviscapum, all species sampled in Fordiophyton formed a strongly supported clade in which two geographical lineages were recovered. The generic placement of F.jinpingense is well supported by phylogenetic analyses and a character combination of 4-merous flowers, distinctly dimorphic stamens and the connectives basally not calcarate. Molecular divergence and morphological evidence indicate that F.jinpingense is well separated from other members of the genus, thus justifying its recognition as a distinct species. Fordiophytonjinpingense is phylogenetically closest to F.repens, but differs markedly from the latter in stem morphology (short, obtusely 4-sided vs. long, 4-angular), habit (erect vs. creeping), leaf size (6-16.5 × 4.5-13 cm vs. 4-7.5 × 4-6.5 cm) and flower number per inflorescence (5-13 vs. 3-6).

The specific status of Melastoma kudoi (Melastomataceae, Melastomeae).

BACKGROUND: Melastoma has undergone rapid species radiation during the last one million years, and circumscription of some species in the genus has remained controversial. Melastoma kudoi, an erect species narrowly endemic to central Taiwan was previously treated as a synonym of M. intermedium, a semicreeping hybrid between the erect species M. candidum and the creeping M. dodecandrum, making its identity questionable. We addressed this question based on molecular and morphological data. RESULTS: Phylogenetic analyses based on nrITS sequence data revealed that M. kudoi is most closely related to M. dodecandrum. Further analyses of six nuclear genes (cam, chi, gapC, gbss, tpi and vr) and two chloroplast markers (trnL-trnF and psbA) showed that M. kudoi is well diverged from its close relatives. Morphologically, it is also easily distinguished from related species by its erect habit, center-positioned stigma, and spreading, basally enlarged hairs on the hypanthium. CONCLUSIONS: Both molecular phylogenetic and morphological data suggest that M. kudoi is well separated from M. intermedium, M. dodecandrum, and O. scaberrima, and should be treated as a distinct species. Taxonomic treatment and detailed description of M. kudoi are provided.

The chloroplast genome of silk floss tree (Ceiba speciosa).

Ceiba speciosa (Malvaceae), also called silk floss tree, is a beautiful and deciduous tree native to tropical and subtropical forests of South America. Its phylogenetic position remains unclear. In this study, the complete chloroplast genome sequence of C. speciosa was reported. Its chloroplast genome size was 160,360 bp, which contains a small single copy (SSC) region of 19,947 bp and a large single copy region (LSC) of 89,393 bp, and two inverted repeats (IRs) of 25,510 bp each. In total, 129 genes were annotated for the chloroplast genome, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis showed that C. speciosa was sister to Bombax ceiba.