Related Species Research Articles

Digest: Scarce pollen resources and asymmetric reproductive isolation.

What mechanisms cause asymmetries in reproductive success in crosses between closely related species that differ in floral style length? Feller et al. (2024) found that in five Phlox species, short-styled species produced smaller pollen grains than long-styled species. The smaller pollen of short-styled species lacked the resources to grow pollen tubes long enough to reach the ovules of long-styled species. This asymmetric pollen-style-length incompatibility may considerably affect patterns of gene flow among species.

Enhanced detection of Pythium insidiosum via lipid profiling with matrix-assisted laser desorption ionization time of flight mass spectrometry

Pythiosis is a severe disease in humans and animals globally, caused by the pathogenic oomycete Pythium insidiosum. Early and accurate detection is crucial for effective treatment, but traditional diagnostic methods have limitations. This study presents an alternative approach using Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for lipid profiling to efficiently identify P. insidiosum. The study involved extracting microbial lipid components using optimized chloroform: methanol biphasic method and creating a lipid profile database with samples from 30 P. insidiosum isolates and 50 various fungi. The methodology was validated on 25 blinded samples for assay detection performance. Unique lipid profiles allowed species-specific identification with high efficiency: scores ≥ 2.682 indicated P. insidiosum, scores ≤ 2.512 suggested fungi, and scores in between pointed to other oomycetes. The assay demonstrated sensitivity, specificity, and accuracy of 100%, 80%, and 88%, respectively, for detecting P. insidiosum. The limited detection specificity was due to false positive samples from closely related Pythium species, which are not a significant clinical concern. The findings show that MALDI-TOF MS lipid profiling can efficiently identify P. insidiosum, offering significant advantages in sample preparation, stability, and reproducibility over protein profile-based methods. This study marks the first instance of lipid profiles being reported for P. insidiosum, paving the way for clinical use in improving accurate detection and facilitating timely treatment interventions.

Study of the Genetic Mechanisms of Siberian Stone Pine (Pinus sibirica Du Tour) Adaptation to the Climatic and Pest Outbreak Stresses Using Dendrogenomic Approach

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms—SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype–dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant’s genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change.

Image-Based Quantitative Analysis of Epidermal Morphology in Wild Potato Leaves

The epidermal leaf patterns of plants exhibit remarkable diversity in cell shapes, sizes, and arrangements, driven by environmental interactions that lead to significant adaptive changes even among closely related species. The Solanaceae family, known for its high diversity of adaptive epidermal structures, has traditionally been studied using qualitative phenotypic descriptions. To advance this, we developed a workflow combining multi-scale computer vision, image processing, and data analysis to extract digital descriptors for leaf epidermal cell morphology. Applied to nine wild potato species, this workflow quantified key morphological parameters, identifying descriptors for trichomes, stomata, and pavement cells, and revealing interdependencies among these traits. Principal component analysis (PCA) highlighted two main axes, accounting for 45% and 21% of variance, corresponding to features such as guard cell shape, trichome length, stomatal density, and trichome density. These axes aligned well with the historical and geographical origins of the species, separating southern from Central American species, and forming distinct clusters for monophyletic groups. This workflow thus establishes a quantitative foundation for investigating leaf epidermal cell morphology within phylogenetic and geographic contexts.

Genetic linkage disequilibrium of deleterious mutations in threatened mammals.

The impact of negative selection against deleterious mutations in endangered species remains underexplored. Recent studies have measured mutation load by comparing the accumulation of deleterious mutations, however, this method is most effective when comparing within and between populations of phylogenetically closely related species. Here, we introduced new statistics, LDcor, and its standardized form nLDcor, which allows us to detect and compare global linkage disequilibrium of deleterious mutations across species using unphased genotypes. These statistics measure averaged pairwise standardized covariance and standardize mutation differences based on the standard deviation of alleles to reflect selection intensity. We then examined selection strength in the genomes of seven mammals. Tigers exhibited an over-dispersion of deleterious mutations, while gorillas, giant pandas, and golden snub-nosed monkeys displayed negative linkage disequilibrium. Furthermore, the distribution of deleterious mutations in threatened mammals did not reveal consistent trends. Our results indicate that these newly developed statistics could help us understand the genetic burden of threatened species.

Development and optimization of the qPCR-based rapid detection method for Chinese species of Sanghuangporus

Sanghuangporus, well known as ‘Sanghuang’, is a macrofungal genus accommodating 11 edible and medicinal species in China. With the prosperous development of ‘Sanghuang’ business in China, the fraudulent practice naming the products of other morphologically and phylogenetically related species as ‘Sanghuang’ happens frequently, which disturbs the market order of ‘Sanghuang’ business. To promote the healthy industrial development of Sanghuangporus and also prevent the loss of this macrofungal resource, we develop a qPCR-based rapid detection method in this study. Internal transcribed spacer sequences of Fuscoporia, Inonotus, Phellinus, Sanghuangporus and Tropicoporus were aligned to design Sanghuangporus-specific amplification primers and probe, which can specifically distinguish all 11 Chinese species of Sanghuangporus from species of other closely related genera. The concentrations of Sanghuangporus-specific primers and probe were optimized as 0.7 μmol/L and 0.5 μmol/L, respectively, where the qPCR has the minimum detectable DNA template concentration of 10-3 ng/μL. In summary, the current qPCR-based detection method was specific, sensitive and rapid for Chinese species of Sanghuangporus.

Intersectional Hybrids of the Relict Species, Box Huckleberry (Gaylussacia brachycera), with Dwarf Huckleberry (Gaylussacia dumosa)

Gaylussacia brachycera (box huckleberry) is a unique relict species and is the monospecific member of Gaylussacia sect. Vitis-idaea. As part of investigations to understand interspecific crossability in Gaylussacia, pollinations were made between evergreen 2x G. brachycera and deciduous 2x G. dumosa (dwarf huckleberry). The primary pollinations succeeded at a low level and produced four viable hybrids. Three of these hybrids had box huckleberry as the female, and one of them, dwarf huckleberry, as the female. Morphologically, these hybrids were distinct from the parents and were generally intermediate. The fertility of the hybrids was low, but one hybrid flowered sufficiently to allow collection of pollen and to backcross it as a male to box huckleberry. Four BC1 hybrids were produced from this cross. The F1 and BC1 hybrids were all verified using simple sequence repeat markers developed for the closely related genus Vaccinium. These hybrids are notable for being the first recorded hybrids of this rare species, G. brachycera, with any other Gaylussacia species, and these hybrids are expected to lead to a better understanding of species relationships both within Gaylussacia and between Gaylussacia and Vaccinium.

A taxonomic monograph of subfamily Scolytinae (Coleoptera: Curculionidae) in the Western Himalaya

We investigated the scolytine fauna of the West Himalayan region of India. The present study combines field samples, museum specimens, and published data to catalog the scolytine diversity. We recognize 57 scolytine species from 15 tribes and 25 genera. Five new species Cryphalus himalayensis sp. nov., Dryocoetes asperatus sp. nov., Ernoporus squamosus sp. nov., Scolytoplatypus denticauda sp. nov., and Hypothenemus ficivorus sp. nov. are described from the region. Previously reported and inadequately characterized species are imaged and redescribed. Two new Indian records, seven new regional records, and fifteen new host records are reported. Keys to genera and photographs of each species are provided to facilitate identification. Mitochondrial COX-1 sequences were generated from some Himalayan species and sequences from GenBank were utilized for comparison with other related species. The current monographic study includes an overview of each species' taxonomic diagnosis, range, and host plants. Furthermore, an updated list of 165 scolytine species, distributed in the Himalaya but excluding its eastern part of Arunachal Pradesh, is also provided.

Microbiome divergence of marine gastropod species separated by the Isthmus of Panama.

The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithium and Cerithideopsis to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis but not Cerithium. These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves.IMPORTANCEWhile considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history.

African Horned Melon (Cucumis metuliferus): Climate‐Resilient Crop and Gene Donor in the Breeding of Major Cucurbits

ABSTRACTAfrican horned melon (Cucumis metuliferus E. Meyer ex Naudin, 2n = 2x = 24) is an under‐researched and under‐utilised cucurbit crop primarily grown for its nutritious fruit. In its centre of diversity, the crop is valued for its relatively high tolerance to insect pests, diseases, drought and heat stress. It is a potential opportunity crop and a valuable source of genes to major Cucumis species, including cucumber (Cucumis sativas L.) and melon (C. melo L.). Its climate resilience and nutrient‐rich fruit provide niche market opportunities. Hence, production and value‐adding will make African horned melon a crop of choice globally. There is a need for an in‐depth investigation into the genetic diversity, breeding and food composition of the crop. Therefore, the objective of this review was to provide perspectives on the production and breeding status of African horned melon to appraise its genetic value for human welfare, strategic production, genetic conservation and breeding of market‐preferred varieties, including closely related Cucumis species. The first section described the botany, production status, germplasm resources and characterisation based on phenotypic and genetic markers. This is followed by breeding progress for biotic and abiotic stress tolerance, utilities and challenges of gene transfer and potential rootstock to Cucumis species, especially cucumber and melon. The review summarised the main breeding goals and approaches, including mutation breeding to fast‐track the development of new varieties. Information presented in the review will guide cultivar design in African horned melon or related cucurbits, aiming for superior agronomic and nutritional quality traits and tolerance to biotic and abiotic stresses.

A new species of Autocrates (Coleoptera: Trictenotomidae) revealed by DNA barcoding and morphological evidence

Autocrates soni sp. nov. is described from Vietnam based on morphological and molecular evidence. This beetle is characterised by reddish-brown pubescence on its ventral side and much shorter setae on its femora compared to the closely related species Autocrates vitalisi Vuillet, 1912. The validity of this new species is strongly supported by DNA barcode data from all known species of the genus Autocrates.

Host species-specific activity of the poxvirus PKR inhibitors E3 and K3 mediate host range function.

The antiviral protein kinase R (PKR) is activated by viral double-stranded RNA and phosphorylates translation initiation factor eIF2α, thereby inhibiting translation and virus replication. Most poxviruses contain two PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), which are determinants of viral host range. The prevailing model for E3 function is that it inhibits PKR through the non-specific sequestration of double-stranded (ds) RNA. Our data revealed that Syrian hamster PKR was resistant to E3, which is at odds with the sequestration model. However, Syrian hamster PKR was still sensitive to K3 inhibition. In contrast, Armenian hamster PKR showed opposite sensitivities, being sensitive to E3 and resistant to K3 inhibition. Mutational analyses of hamster PKRs showed that sensitivity to E3 inhibition was largely determined by the region linking the dsRNA-binding domains and the kinase domain of PKR, whereas two amino acid residues in the kinase domain (helix αG) determined sensitivity to K3. The expression of PKRs in congenic cells showed that Syrian hamster PKR containing the two Armenian hamster PKR residues in helix αG was resistant to wild-type VACV infection and that cells expressing either hamster PKR recapitulated the phenotypes observed in species-derived cell lines. The observed resistance of Syrian hamster PKR to E3 explains its host range function and challenges the paradigm that dsRNA-binding PKR inhibitors mainly act by the sequestration of dsRNA.IMPORTANCEThe molecular mechanisms that govern the host range of viruses are incompletely understood. We show that the host range functions of E3 and K3, two host range factors from vaccinia virus, are a result of species-specific interactions with the antiviral protein kinase R (PKR) and that PKR from closely related species displayed dramatic differences in their sensitivities to these viral inhibitors. The current model for E3-mediated PKR inhibition is that E3 non-specifically sequesters double-stranded (ds) RNA to prevent PKR activation. This model does not predict species-specific sensitivity to E3; therefore, our data suggest that the current model is incomplete and that dsRNA sequestration is not the primary mechanism for E3 activity.

A type VI secretion system in Burkholderia species cenocepacia and orbicola triggers distinct macrophage death pathways independent of the pyrin inflammasome.

The Burkholderia cepacia complex contains opportunistic pathogens that cause chronic infections and inflammation in the lungs of people with cystic fibrosis. Two closely related species within this complex are Burkholderia cenocepacia and the recently classified Burkholderia orbicola. B. cenocepacia and B. orbicola encode a type VI secretion system and the effector TecA, which is detected by the pyrin/caspase-1 inflammasome, and triggers macrophage inflammatory death. We previously showed that the pyrin inflammasome was dispensable for lung inflammation in mice infected with B. orbicola AU1054, indicating this species activates an alternative pathway of macrophage inflammatory death. Notably, B. cenocepacia strains J2315 and K56-2 can damage macrophage phagosomes, and K56-2 triggers activation of the caspase-11 inflammasome, which detects cytosolic lipopolysaccharide. Here, we investigated inflammatory cell death in pyrin- (Mefv-/-) or caspase-1/caspase-11- (Casp1/11-/-) deficient mouse macrophages infected with B. cenocepacia J2315 or K56-2 or B. orbicola AU1054 or PC184. Macrophage inflammatory death was measured by cleavage of gasdermin D protein, the release of cytokines IL-1α and IL-1β, and plasma membrane rupture. We found that J2315 and K56-2 are detected by the caspase-11 inflammasome in Mefv-/- macrophages, resulting in IL-1β release. By contrast, inflammasome activation was not detected in Mefv-/- macrophages infected with AU1054 or PC184. Instead, AU1054 triggered an alternative macrophage inflammatory death pathway that required TecA and resulted in plasma membrane rupture and IL-1α release. Structural modeling of TecA orthologs in B. cenocepacia and B. orbicola suggested that amino acid changes in the latter may underlie its ability to trigger a non-inflammasome macrophage death pathway.

Differences in within-plant oviposition preferences and immature survival between Orius predators and the importance of spatial availability of prey.

Oviposition preferences of plant-feeding predators remain a complex topic, as such omnivores choose oviposition sites by assessing both plant characteristics and the quality and quantity of nearby animal food sources. Orius predators are omnivores that oviposit endophytically, thus plant characteristics play an important role in their oviposition choices. In this study, we assessed the oviposition and foraging preferences of O. laevigatus and O. majusculus on vegetative and flowering chrysanthemum plants, and assessed the survival of their offspring on differently aged tissues. Our results show a preference of O. laevigatus for young and tender chrysanthemum tissues, where the survival of the nymphs was longer on a plant diet. In contrast, O. majusculus selected older plant parts when laying its eggs, and nymphs did not survive long on any of the plant tissues offered. The foraging activity of Orius females for animal prey (Ephestia kuehniella eggs) did not reveal any specific pattern for either of the two predators. Furthermore, we tested the plasticity of the within-plant oviposition preferences of O. laevigatus, by offering sentinel prey (E. kuehniella eggs) on distinct plant parts. We found that more eggs were laid in older plant tissue when animal prey was offered lower on the plant. Overall, our findings show that oviposition choices of Orius predators are based on a dynamic interplay between plant characteristics, presence of animal and/or floral food sources among other factors, and that differences may well occur between closely related species based on the importance of plant resources in their diet.

Characterization of gut microbiota dynamics in an Alzheimer’s disease mouse model through clade-specific marker-based analysis of shotgun metagenomic data

Alzheimer’s disease (AD) is a complex neurodegenerative disorder significantly impairing cognitive faculties, memory, and physical abilities. To characterize the modulation of the gut microbiota in an in vivo AD model, we performed shotgun metagenomics sequencing on 3xTgAD mice at key time points (i.e., 2, 6, and 12 months) of AD progression. Fecal samples from both 3xTgAD and wild-type mice were collected, DNA extracted, and sequenced. Quantitative taxon abundance assessment using MetaPhlAn 4 ensured precise microbial community representation. The analysis focused on species-level genome bins (SGBs) including both known and unknown SGBs (kSGBs and uSGBs, respectively) and also comprised higher taxonomic categories such as family-level genome bins (FGBs), class-level genome bins (CGBs), and order-level genome bins (OGBs). Our bioinformatic results pinpointed the presence of extensive gut microbial diversity in AD mice and showed that the largest proportion of AD- and aging-associated microbiome changes in 3xTgAD mice concern SGBs that belong to the Bacteroidota and Firmicutes phyla, along with a large set of uncharacterized SGBs. Our findings emphasize the need for further advanced bioinformatic studies for accurate classification and functional analysis of these elusive microbial species in relation to their potential bridging role in the gut-brain axis and AD pathogenesis.

Pheidole praehistorica sp. nov., a new addition to spiny ants of the genus Pheidole Westwood, 1839 (Formicidae, Myrmicinae) from Oligo–Miocene Mexican amber

A fossil species of ant, Pheidole praehistorica sp. nov. (Hymenoptera, Formicidae, Myrmicinae), is described and illustrated from the late Oligocene and early Miocene amber-bearing beds of Mexico. The type material comprises five amber inclusions from the Simojovel site in Chiapas. Pheidole praehistorica is recognized by having compound eyes positioned mesad on the head and protruded laterally from the head’s margins; pronotum long, forming a neck, with a pair of spines directed dorsolaterally; mesonotal groove deep forming a more or less U-shape concavity in lateral view; dorsal and declivitous faces of the propodeum well differentiated, comprising an approximately 90 degrees angle; propodeum with a pair of long spines; peduncle of the petiole long, as long as the spines of the propodeum. A phylogenetic analysis was also performed using Formica integroides, Camponotus chartifex, Dolichoderus spurius, Cephalotes minutus and Atta mexicana to assess the relationships of P. praehistorica with its fossil spiny congeners from Dominican amber and closely related extant species. The results show close morphological and phylogenetic affinities between the fossil ant P. praehistorica with P. primigenia and P. tethepa from Dominican amber, which may suggest that the shared spinescence character in Pheidole has a probable New World ancestry. The new record of P. praehistorica in the Oligo–Miocene strata of southernmost North America provides further evidence for the ancient distribution of spiny ants of the genus Pheidole in the New World.

The oldest tadpole reveals evolutionary stability of the anuran life cycle.

Anurans are characterized by a biphasic life cycle, with an aquatic larval (tadpole) stage followed by an adult (frog) stage, both connected through the metamorphic period in which drastic morphological and physiological changes occur1. Extant tadpoles exhibit great morphological diversity and ecological relevance2, but their absence in the pre-Cretaceous fossil record (older than 145 million years) makes their origins and early evolution enigmatic. This contrasts with the postmetamorphic anuran fossil record that dates back to theEarly Jurassic and with closely related species in the Late Triassic (around 217-213 million years ago (Ma))3. Here we report a late-stage tadpole of the stem-anuran Notobatrachus degiustoi from the Middle Jurassic of Patagonia (around 168-161 Ma). This finding has dual importance because it represents the oldest-known tadpole and, to our knowledge, the first stem-anuran larva. Its exquisite preservation, including soft tissues, shows features associated with the filter-feeding mechanism characteristic of extant tadpoles4,5. Notably, both N. degiustoi tadpole and adult reached a large size, demonstrating that tadpole gigantism occurred among stem-anurans. This new discovery reveals that a biphasic life cycle, with filter-feeding tadpoles inhabiting aquatic ephemeral environments, was already present in the early evolutionary history of stem-anurans and has remained stable for at least 161 million years.

Morphology and phylogeny reveal a new ramarioid species of Phaeoclavulina (Gomphaceae, Basidiomycota) from Yunnan Province, China

During a survey of coral mushrooms in Yunnan Province, China, yellow, cylindrical, and coral-shaped basidiomata were collected and preliminarily identified as a Phaeoclavulina species. Phylogenetic analyses of combined ITS1–5.8S–ITS2 and LSU sequences support our collections positioning within Phaeoclavulina sister lineage to P. carovinacea strains with 58% BS and 0.95 PP statistical support. Our Phaeoclavulina collection is characterized by verrucose, truncate (volcanic) spines in spores, and clamp connections that differ from closely related species. Phylogenetic analysis results and morphological comparisons support our collection as a distinct new species of Phaeoclavulina (P. yunnanensis). The new species is described and illustrated, and the results of the phylogenetic analysis are provided.

Complete Chloroplast Genome of Crassula aquatica: Comparative Genomic Analysis and Phylogenetic Relationships

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired.

First De Novo genome assembly and characterization of Gaultheria prostrata

Gaultheria Kalm ex L. (Ericaceae), a type of evergreen shrub, known as a natural source of methyl salicylate, possesses rich germplasm resources, strong habitat adaptability, significant ornamental value, and noteworthy pharmacological activities. However, due to the paucity of whole genomic information, genetically deep research in these areas remains limited. Consequently, we intend to obtain genome data through high-throughput sequencing, gene annotation, flow cytometry, transcription factors prediction and genetic marker analysis for a representative species of this genus, with Gaultheria prostrata selected for our study. In this study, we preliminarily obtained the genome of G. prostrata through next-generation sequencing methods. Utilizing 47.94 Gb of high-quality sequence data (108.95× coverage), assembled into 114,436 scaffolds, with an N50 length of 33,667 bp. The genome size assembled by SOAPdenovo, approximately 417 Mb, corresponded closely to predictions by flow cytometry (440 Mb) and k-mer analysis (447 Mb). The genome integrity was evaluated using BUSCO with 91%. The heterozygosity ratio was 0.159%, the GC content was 38.85%, and the repetitive regions encompassed over 34.6% of the genome. A total of 26,497 protein-coding genes have been predicted and annotated across Nr, Swissprot, GO, KEGG, and Pfam databases. Among these, 14,377 and 2,387 genes received functional annotation in Nr and Swissprot, respectively; 21,895, 24,424, and 22,330 genes were similarly annotated in GO, KEGG, and Pfam. Moreover, A total of 279,785 SSRs were identified and 345,270 primers for these SSRs were designed. Within the various nucleotide types of SSRs, AG/CT and AAG/CTT constituted the predominant dinucleotide and trinucleotide repeat types in G. prostrata. In addition, 1,395 transcription factors (TFs) from 75 TF families, 462 transcription regulators (TRs) from 33 TR families and 840 protein kinase (PKs) from 118 PK families were identified in this genome. We also performed phylogenetic analyses of G. prostrata and related species, including estimation of divergence times and expansion and contraction analyses, followed by positive selection analyses of orthologous gene pairs of G. prostrata and its close relative Vaccinium corymbosum. These results provide a reference for in-depth study of genus Gaultheria, contributing to future functional and comparative genomics analyses and providing supporting data for the development of molecular markers.