Conservation priorities for endangered trees facing multiple threats around the world.

Trees are vital to the survival of numerous species and to forest ecosystem functioning. However, the current distribution, vulnerability to extinction, and conservation priorities of globally endangered trees are not well known. We mapped the global distribution of 1686 tree species listed as endangered on the International Union for the Conservation of Nature Red List and identified conservation priority for them based on species richness, life-history traits, evolutionary distinctiveness, future climate change, and intensity of human activities. We also evaluated the impacts of various threats to these endangered tree species and evaluated the effectiveness of their protection based on the percentage of the species' range inside protected areas. The worldwide distribution of endangered trees, from the tropics through temperate zones, was uneven. Most endangered tree species were not protected in their native ranges, and only 153 species were fully protected. Hotspots of tree diversity occurred primarily in the tropics, and 79.06% of these were highly vulnerable to threats. We identified 253 areas of high priority for the conservation of endangered trees that are highly threatened and insufficiently protected. In particular, 43.42% of unprotected tree species in priority areas lacked recommended conservation measures or had no associated conservation plan. The priority conservation areas and unprotected trees we identified serve as a guideline for future management underpinning the post-2020 global biodiversity framework.

Prioridades de conservación para los árboles amenazados que enfrentan múltiples amenazas en todo el mundo Resumen Los árboles son vitales para la supervivencia de numerosas especies y para el funcionamiento de los ecosistemas forestales. Sin embargo, no se conoce muy bien la distribución actual, vulnerabilidad a la extinción y prioridades de conservación de los árboles amenazados a nivel mundial. Mapeamos la distribución global de 1686 especies de árboles catalogadas como en peligro por la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza e identificamos su prioridad de conservación con base en la riqueza de especies, características de historia de vida, singularidad evolutiva, cambio climático futuro e intensidad de las actividades humanas. También evaluamos el impacto de varias amenazas sobre estas especies y analizamos la efectividad de su protección con base en el porcentaje de la distribución de la especie ubicado dentro de un área protegida. La distribución mundial de árboles en peligro, desde los trópicos y hasta las zonas templadas, fue desigual. La mayoría de las especies no estaban protegidas dentro de su distribución nativa y sólo 153 especies contaban con protección completa. Los puntos calientes de diversidad de árboles se ubicaron principalmente en los trópicos, y el 79.06% de estos tenían una vulnerabilidad alta ante las amenazas. Identificamos 253 áreas de gran prioridad para la conservación de los árboles en peligro que están amenazados y con poca protección. En particular, el 43.42% de las áreas sin protección dentro de las áreas prioritarias no contaban con las medidas recomendadas de conservación o no tenían asociado un plan de conservación. Las áreas prioritarias de conservación y los árboles sin protección que identificamos son una pauta para futuros manejos que apuntalan el marco de trabajo post-2020 para la biodiversidad.

Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated.

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.

Abiotic Niche Divergence of Hybrid Species from Their Progenitors.

AbstractAlthough more frequently discussed recently than previously, the role of ecology in homoploid hybrid and allopolyploid speciation has not been subjected to comparative analysis. We examined abiotic niche divergence of 22 assumed homoploid hybrid species and 60 allopolyploid species from that of their progenitors. Ecological niche modeling was employed in an analysis of each species' fundamental niche, and ordination methods were used in an analysis of realized niches. Both analyses utilized 100,000 georeferenced records. From estimates of niche overlap and niche breadth, we identified for both types of hybrid species four niche divergence patterns: niche novelty, niche contraction, niche intermediacy, and niche expansion. Niche shifts involving niche novelty were common and considered likely to play an important role in the establishment of both types of hybrid species, although more so for homoploid hybrid species than for allopolyploid species. Approximately 70% of homoploid hybrid species versus 37% of allopolyploid species showed shifts in the fundamental niche from their parents, and ∼86% versus ∼52%, respectively, exhibited shifts in the realized niche. Climate was shown to contribute more than soil and landform to niche shifts in both types of hybrid species. Overall, our results highlight the significance of abiotic niche divergence for hybrid speciation, especially without genome duplication.

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species.

BACKGROUND: The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. RESULTS: The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). CONCLUSION: The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes.

Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth. To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses, there is a need for convenient and accurate toolkits. To meet this need, we developed WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi). As an example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

Warming-induced increase in carbon uptake is linked to earlier spring phenology in temperate and boreal forests.

Under global warming, advances in spring phenology due to rising temperatures have been widely reported. However, the physiological mechanisms underlying the advancement in spring phenology still remain poorly understood. Here, we investigated the effect of temperature during the previous growing season on spring phenology of current year based on the start of season extracted from multiple long-term and large-scale phenological datasets between 1951 and 2018. Our findings indicate that warmer temperatures during previous growing season are linked to earlier spring phenology of current year in temperate and boreal forests. Correspondingly, we observed an earlier spring phenology with the increase in photosynthesis of the previous growing season. These findings suggest that the observed warming-induced earlier spring phenology is driven by increased photosynthetic carbon assimilation in the previous growing season. Therefore, the vital role of warming-induced changes in carbon assimilation should be considered to accurately project spring phenology and carbon cycling in forest ecosystems under future climate warming.

Diversity patterns and conservation gaps of Magnoliaceae species in China.

Magnoliaceae, a primitive group of angiosperms and distinguished ornamental plants with more than 100 species in China, is one of the most threatened plant family in the wild due to logging, habitat loss, over-collection and climate change. To provide a scientific guide of its conservation for policymakers, we explore the diversity patterns of 114 Magnoliaceae species in China using three diversity indices (species richness, weighted endemism, ß-diversity) with a spatial resolution of 10 km by 10 km. Two methods, the top 5% richness algorithm and complementary algorithm, are used to identify diversity hotspots. Conservation gaps are recognized by overlapping the diversity hotspots with Chinese nature reserves. Our results indicate that Magnoliaceae species richness and weighted endemism are high in tropical to subtropical low montane forests in southern China, exceptionally high in southernmost Yunnan and boundary of Guizhou, Guangxi and Hunan. The ß-diversity are scattered in southern China, suggesting a different species composition among grid cells. We identify 2524 grids as diversity hotspots for Magnoliaceae species in China, with 24 grids covered by three diversity indices (first-level diversity hotspots), 561 grids covered by two indices (second-level diversity hotspots) simultaneously and 1939 grids (76.8%) covered by only one index (third-level diversity hotspots). The first-level diversity hotspots include over 70% of the critically endangered Magnoliaceae species and are the priority areas for Magnoliaceae conservation. However, only 24% of the diversity hotspots fall in nature reserves and only ten grids are from the first-level diversity hotspots. Zhejiang, Guizhou and Fujian have less than 20% of diversity hotspots covered by nature reserves and need attention in future Magnoliaceae conservation. Using multiple diversity indices and algorithms, our study identifies diversity hotspots and conservation gaps and provides scientific basis for Magnoliaceae conservation in future.

Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China.

Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.

Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation.

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

Contrasting temporal variations in responses of leaf unfolding to daytime and nighttime warming.

Earlier spring phenological events have been widely reported in plants under global warming. Recent studies reported a slowdown in the warming-induced advanced spring phenology in temperate regions. However, previous research mainly focused on daily mean temperature, thus neglecting the asymmetric phenological responses to daytime and nighttime temperature. Using long-term records of leaf unfolding in eight deciduous species at 1300 sites across central Europe, we assessed and compared the effects of daytime temperature, nighttime temperature, and photoperiod on leaf unfolding during 1951-1980 and 1981-2013. Although leaf unfolding was advanced by daytime warming during 1951-2013, the advancing responses of leaf unfolding significantly decreased from 1951-1980 to 1981-2013 due to a lower accumulation of chilling units by daytime warming. Nighttime warming delayed leaf unfolding during 1951-1980 but advanced it during 1981-2013 due to a higher accumulation of chilling units by nighttime warming. In contrast, critical daylength and plasticity of leaf unfolding dates remained unchanged between 1951 and 2013. Our study provided evidence that daytime warming instead of nighttime warming accounts for the slowdown in the advancing spring phenology and implied that nighttime warming-induced earlier spring phenology may be buffering the slowdown of the advanced spring phenology by daytime warming. The response of spring phenology to nighttime temperature may override that to daytime temperature under the actual trends in global warming.

The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae.

Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relationships of Crassulaceae remain partially obscured. Here, we report nine newly sequenced chloroplast genomes, which comprise several key lineages of Crassulaceae. Our comparative analyses and positive selection analyses of Crassulaceae species indicate that the overall gene organization and function of the chloroplast genome are highly conserved across the family. No positively selected gene was statistically supported in Crassulaceae lineage using likelihood ratio test (LRT) based on branch-site models. Among the three subfamilies of Crassulaceae, our phylogenetic analyses of chloroplast protein-coding genes support Crassuloideae as sister to Kalanchoideae plus Sempervivoideae. Furthermore, within Sempervivoideae, our analyses unambiguously resolved five clades that are successively sister lineages, i.e., Telephium clade, Sempervivum clade, Aeonium clade, Leucosedum clade, and Acre clade. Overall, this study enhances our understanding of the infrafamilial relationships and the conservation of chloroplast genomes within Crassulaceae.

A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis.

Camptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Here, we report a high-quality, chromosome-level C. acuminata genome assembly. We find that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. Comparing with Catharanthus roseus, the loganic acid O-methyltransferase (LAMT) in C. acuminata fails to convert loganic acid into loganin. Instead, two secologanic acid synthases (SLASs) convert loganic acid to secologanic acid. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contribute greatly to the camptothecin biosynthesis in C. acuminata. Our results emphasize the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.

Chromosome-level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis.

Sichuan pepper is a commonly used spice in Asian cuisine. Sanshools and wgx-50/gx-50 isolated from it have been shown to possess a wide spectrum of medicinal properties. Here we generated a chromosome-level genome assembly of one Sichuan pepper species Zanthoxylum armatum characterized by drought tolerance and apomixis. Analyses of functionally related genes suggested that increased gene copy number and expression level of drought-tolerant genes might play an important role in improving drought tolerance of Z. armatum. Moreover, a gene encoding an RWP-RK domain-containing protein was shown to contribute to apomixis in Z. armatum, which was further characterized by overexpression in Arabidopsis thaliana. Furthermore, based on gene homology searching and co-expression patterns of metabolite concentration and gene expressions, we identified a number of candidate genes involved in the biosynthesis of sanshools and wgx-50/gx-50. Taken together, our results yield valuable insights for understanding the evolution of apomixis, drought tolerance, and alkaloid biosynthesis in Z. armatum.

Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis.

BACKGROUND: Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment. RESULTS: Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as "TC box"). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment. CONCLUSIONS: Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a "TC box".

Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae).

Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.

A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae).

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales.

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].

A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance.

Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi-C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.