Chromosome-level genome assembly of Helwingia omeiensis: the first genome in the family Helwingiaceae.

Helwingia, a shrub of the monotypic cosmopolitan family Helwingiaceae, is distinguished by its inflorescence, in which flowers are borne on the midrib of the leaf-a trait not commonly observed in related plant families. Previous studies have investigated the development of this unusual structure using comparative anatomical methods. However, the scarcity of genomic data has hindered our understanding of the origins and evolutionary history of this uncommon trait at the molecular level. Here, we report the first high-quality genome of the family Helwingiaceae. Assembled using HiFi sequencing and Hi-C technologies, the genome of H. omeiensis is anchored to 19 chromosomes, with a total length of 2.75 Gb and a contig N50 length of 6.78 Mb. The BUSCO completeness score of the assembled genome was 98.2%. 53,951 genes were identified, of which 99.7% were annotated in at least one protein database. The high-quality reference genome of H. omeiensis provides an essential genetic resource and sheds light on the phylogeny and evolution of specific traits in the family Helwingiaceae.

A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model.

BACKGROUND: Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize. RESULTS: We report the sequencing and assembly of the E. salsugineum (Shandong accession) genome using long-read sequencing and chromosome conformation capture data. We generated Oxford Nanopore long reads at high depth (> 60X) of genome coverage with additional short reads for error correction. The new assembly has a total size of 295.5 Mb with 52.8% repetitive sequences, and the karyotype of E. salsugineum is consistent with the ancestral translocation Proto-Calepineae Karyotype structure in both order and orientation. Compared with previous assemblies, this assembly has higher contiguity, especially in the centromere region. Based on this new assembly, we predicted 25,399 protein-coding genes and identified the positively selected genes associated with salt and drought stress responses. CONCLUSION: The new genome assembly will provide a valuable resource for future genomic studies and facilitate comparative genomic analysis with other plants.

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.

Out of the Qinghai-Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae).

Numerous high-elevation alpine plants of the Qinghai-Tibet Plateau (QTP) also have disjunct distribution in adjacent low-altitude mountains. The out-of-QTP versus into-the-QTP hypothesis of alpine plants provide strong evidence for the highly disputed assumption of the massive ice sheet developed in the central plateau during the Last Glacial Maximum (LGM). In this study, we sequenced the genomes of most known populations of Megadenia, a monospecific alpine genus of Brassicaceae distributed primarily in the QTP, though rarely found in adjacent low-elevation mountains of north China and Russia (NC-R). All sequenced samples clustered into four geographic genetic groups: one pair was in the QTP and another was in NC-R. The latter pair is nested within the former, and these findings support the out-of-QTP hypothesis. Dating the four genetic groups and niche distribution suggested that Megadenia migrated out of the QTP to adjacent regions during the LGM. The NC-R group showed a decrease in the effective population sizes. In addition, the genes with high genetic divergences in the QTP group were mainly involved in habitat adaptations during low-altitude colonization. These findings reject the hypothesis of development massive ice sheets, and support glacial survival of alpine plants within, as well as further migration out of, the QTP.

The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis.

Gentiana dahurica Fisch. is a perennial herb of the family Gentianaceae. This species is used as a traditional Tibetan medicine because of its rich gentiopicroside constituents. Here, we generate a high-quality, chromosome-level genome of G. dahurica with a total length of 1,416.54 Mb. Comparative genomic analyses showed that G. dahurica shared one whole-genome duplication (WGD) event with Gelsemium sempervirens of the family Gelsemiaceaei and had one additional species-specific WGD after the ancient whole-genome triplication with other eudicots. Further transcriptome analyses identified numerous enzyme coding genes and the transcription factors related to gentiopicroside biosynthesis. A set of candidate cytochrome P450 genes were identified for being involved in biosynthetic shifts from swertiamarin to gentiopicroside. Both gene expressions and the contents measured by high-performance liquid chromatography indicated that the gentiopicrosides were mainly synthesized in the rhizomes with the highest contents. In addition, we found that two above-mentioned WGDs, contributed greatly to the identified candidate genes involving in gentiopicroside biosynthesis. The first reference genome of Gentianaceae we generated here will definitely accelerate evolutionary, ecological, and pharmaceutical studies of this family.

A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation.

It remains largely unknown how plants adapt to high-altitude habitats. Crucihimalaya (Brassicaceae) is an alpine genus occurring in the Qinghai-Tibet Plateau characterized by cold temperatures and strong ultraviolet radiation. Here, we generated a chromosome-level genome for C. lasiocarpa with a total size of 255.8 Mb and a scaffold N50 size of 31.9 Mb. We first examined the karyotype origin of this species and found that the karyotype of five chromosomes resembled the ancestral karyotype of the Brassicaceae family, while the other three showed strong chromosomal structural variations. In combination with the rough genome sequence of another congener (C. himalaica), we found that the significantly expanded gene families and positively selected genes involved in alpine adaptation have occurred since the origin of this genus. Our new findings provide valuable information for the chromosomal karyotype evolution of Brassicaceae and investigations of high-altitude environment adaptation of the genus.

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.

Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan.

Previous studies demonstrated that lifelong treatment with a slow H2S releasing donor extends yeast chronological lifespan (CLS), but it is not clear when the action of H2S benefits to CLS during yeast growth. Here, we show that short H2S treatments by using NaHS as a fast H2S releasing donor at 96 hours after inoculation extended yeast CLS while NaHS treatments earlier than 72 hours after inoculation failed to do so. To reveal the mechanism, we analyzed the transcriptome of yeast cells with or without the early and late NaHS treatments. We found that both treatments had similar effects on pathways related to CLS regulation. Follow-up qPCR and ROS analyses suggest that altered expression of some antioxidant genes by the early NaHS treatments were not stable enough to benefit CLS. Moreover, transcriptome data also indicated that some genes were regulated differently by the early and late H2S treatment. Specifically, we found that the expression of YPK2, a human SGK2 homolog and also a key regulator of the yeast cell wall synthesis, was significantly altered by the late NaHS treatment but not altered by the early NaHS treatment. Finally, the key role of YPK2 in CLS regulation by H2S is revealed by CLS data showing that the late NaHS treatment did not enhance the CLS of a ypk2 knockout mutant. This study sheds light on the molecular mechanism of CLS extension induced by H2S, and for the first time addresses the importance of H2S treatment timing for lifespan extension.

Hybrid speciation via inheritance of alternate alleles of parental isolating genes.

It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae).

Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high-confidence protein-coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11-36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto-Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end-to-end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.

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.

The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication.

Megacarpaea delavayi (Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000-4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome of M. delavayi is 883 Mb, and 61.59% of the genome is composed of repeat sequences. Annotation of the genome identified a total of 41,114 protein-coding genes. We found that M. delavayi experienced an independent whole-genome duplication (WGD), paralleling those independent WGDs in Iberis, Biscutella, and Anastatica in the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genus Megacarpaea within the expanded lineage II of the family and resolved its basal divergence to a subclade consisting of Anastatica, Iberis, and Biscutella. Species-specific and fast-evolving genes in M. delavayi are mainly involved in "DNA repair" and "response to UV-B radiation." These genetic changes may together help this species survive in high-altitude environments. The reference genome reported here provides a valuable resource for studying adaptation of this and other alpine plants to the high-altitude habitats.

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome.

Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88 Mb and scaffold N50 = 36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 high-confidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants.

Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex.

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.

The complete chloroplast genome of Gentaina urnula (Gentianaceae).

Gentiana urnula, is an alpine medicinal endemic to the Qinghai-Tibetan Plateau. In this study, the complete chloroplast DNA sequence of G. urnula was assembled，and its genome is 149,064 bp in length, including a large single-copy region (LSC) of 81,158 bp and a small single-copy region (SSC) of 17,034 bp, which was separated by a pair of 25,436 bp inverted repeat regions (IRs). A total of 130 genes are detected, including 86 protein-coding genes, 37 tRNA genes, and 7 rRNA genes. The complete chloroplast genomes of G. urnula will help to study the genetic diversity and phylogenetic analysis of Gentianales.

The complete chloroplast genome of Swertia cordata.

Swertia cordata, a herbaceous plant, has been used in medicines as an alternative febrifuge and anthelmintic. In this study, the complete chloroplast DNA sequence of S. cordata was assembled. It is 153,429 bp in length, including a large single-copy region of 83,613 bp and a small single-copy region of 18,038 bp separated by a pair of inverted repeat regions of 25,889 bp each. A total of 129 genes are detected, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The complete chloroplast genome of S. cordata will help to study the genetic diversity and phylogenetic analysis of Swertia.

Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent.

The wisent or European bison is the largest European herbivore and is completely cross-fertile with its American relative. However, mtDNA genome of wisent is similar to that of cattle, which suggests that wisent emerged as a hybrid of bison and an extinct cattle-like species. Here, we analyzed nuclear whole-genome sequences of the bovine species, and found only a minor and recent gene flow between wisent and cattle. Furthermore, we identified an appreciable heterogeneity of the nuclear gene tree topologies of the bovine species. The relative frequencies of various topologies, including the mtDNA topology, were consistent with frequencies of incomplete lineage sorting (ILS) as estimated by tree coalescence analysis. This indicates that ILS has occurred and may well account for the anomalous wisent mtDNA phylogeny as the outcome of a rare event. We propose that ILS is a possible explanation of phylogenomic anomalies among closely related species.

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process.

An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai-Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected from 34 populations of the three Picea species from their core distributions in the QTP. Phylogenetic, principal component and admixture analyses of nuclear SNPs showed the species to be delimited genetically and that P. purpurea was admixed with approximately 60% of its ancestry derived from P. wilsonii and 40% from P. likiangensis. Coalescent simulations revealed the best-fitting model of origin involved formation of an intermediate hybrid lineage between P. likiangensis and P. wilsonii approximately 6 million years ago (mya), which backcrossed to P. wilsonii to form P. purpurea approximately one mya. The intermediate hybrid lineage no longer exists and is referred to as a "ghost" lineage. Our study emphasizes the power of population genomic analysis combined with coalescent analysis for reconstructing the stages involved in the origin of a homoploid hybrid species over an extended period. In contrast to other studies, we show that these stages can in some instances span a relatively long period of evolutionary time.

Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum.

The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long-distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E. salsugineum. Our population genomic data indicate that E. salsugineum migrated "out of the Altai region" at least three times to colonize northern China, northeast Russia and western China. It then expanded its distribution into North America independently from northeast Russia and northern China, respectively. The species colonized northern China around 33.7 thousand years ago (kya) and underwent a considerable expansion in range size approximately 7-8 kya. The western China lineage is likely a hybrid derivative of the northern China and Altai lineages, originating approximately 25-30 kya. Deleterious alleles accumulated in a stepwise manner from (a) Altai to northern China and North America and (b) Altai to northeast Russia and North America. In summary, E. salsugineum dispersed from Asia to North America and deleterious mutations accumulated in a stepwise manner during the expansion of the species' distribution.