Phylogenetic Research Articles

Description of the new species Mallomonas okhapkinii (Synurales, Chrysophyceae) based on morphological and molecular data

This paper describes a new species of Mallomonas discovered in a swamp area in Russia. The species was identified based on scale morphology, examined using scanning and transmission electron microscopy, and subjected to molecular analysis. The new species, Mallomonas okhapkinii sp. nov., belongs to the section Planae and is most similar in scale and bristle ultrastructure to M. matvienkoae sensu stricto. Phylogenetic analysis, performed using a concatenated dataset of nuclear-encoded small subunit rRNA and plastid-encoded rbcL genes, revealed that the strains of the new species form a distinct clade with high statistical support, closely related to the clade of M. paragrandis and M. sorohexareticulata. This species was found in only one habitat.

Aedes (Georgecraigius) epactius from Zacatecas and Chihuahua Mexico: New Geographical Distribution and Altitude Records

Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional record of Ae. epactius in Zacatecas and provides evidence of the highest altitude in the Americas, including Mexico. The geographical distribution of Ae. epactius in Mexico was reviewed, and the COX1 analysis, using phylogenetic Bayesian analysis to confirm species identification, was performed.

Multiple Maternal Lineages of <i>Strauchbufo raddei</i> (Strauch, 1876) in Mongolia Revealed by Mitochondrial DNA

The Mongolian toad Strauchbufo raddei (Strauch, 1876) is one of widely distributed and dominated amphibian species in eastern Asian, including Mongolia. In this study, we amplified and sequenced a total of 50 samples of S. raddei, from three main regions in its Mongolian distribution range namely, Northern, Eastern, and Gobi regions. Our phylogenetic trees (Bayesian inference; BI and time-calibrated) and network analysis clearly support presence of multiple maternal mitochondrial DNA lineages for S. raddei in Mongolia. As expected, samples from these three regions were clustered separately in BI tree (Bayesian posterior probability (BPP 0.52). In addition, the population specific haplotypes, estimated genetic distances (e.g. uncorrelated p distance; ranged from 1% to 25%) and hierarchical AMOVA suggested relatively strong population genetic structure of S. raddei across Mongolia. Time-calibrated tree and ancestral range analysis showed that the first colonization of S. raddei may have occurred in Northern part of Mongolia approximately 9.63 mya, then dispersed over other parts of the country. Estimated approximate time for crossing event of S. raddei over dry steppe and semi-desert regions in Mongolia was 5.02 – 2.50 mya. Finally, high level of genetic diversity (overall; haplotype diversity, Hd = 0.93; nucleotide diversity, π = 0.011) of S. raddei were observed in Mongolia. Importantly, through this study, we contributed to closing sampling gaps in distribution range of S. raddei in Eastern Asia, which is key to better understanding species history, as well as describing cryptic lineages.

Identification of putative genes for caffeoylated flavonoid glycoside biosynthesis in Pseudognaphalium affine

Pseudognaphalium affine (D. Don) Anderberg, commonly found in East Asia, has extensive applications as both a traditional medicine and a vegetable in China. The caffeoylated flavonoid glycosides produced by P. affine exhibit remarkable anti-complement activities. Although these compounds have potential therapeutic value, the biosynthetic pathway responsible for their production remains largely unknown. To elucidate the key catalytic steps involved in caffeoylated flavonoid glycoside biosynthesis, we conducted a comprehensive analysis of the full-length transcriptome of P. affine. Further phylogenetic tree analysis predicted potential UDP glycosyltransferase (UGT) and BAHD acyltransferase (BAHD-AT) related with caffeoylated flavonoid glycoside biosynthesis. Subsequently, enzyme assay led to the discovery of PaUGT23 as a key enzyme responsible for the glycosylation of hydroxy groups in flavonoids, resulting in the formation of luteolin-4′-O-glucoside, luteolin-7-O-glucoside, quercetin-4′-O-glucoside, quercetin-7-O-glucoside, and apigenin-7-O-glucoside, while PaBAHD21 was found to catalyze the caffeoylation of flavonoid glycosides, resulting in the formation of luteolin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside, quercetin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside, apigenin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside and apigenin 7-O-β-D-(6″-E-caffeoyl)-glucopyranoside. Moreover, their catalytic activities were verified in vivo by transient transfection experiment. This study presents the first comprehensive analysis of the full-length transcriptome in P. affine, providing significant insights into the biosynthesis and accumulation mechanisms of bioactive caffeoylated flavonoid glycosides.

Genome-Wide Identification and Analysis of Phospholipase C Gene Family Reveals Orthologs, Co-Expression Networks, and Expression Profiling Under Abiotic Stress in Sorghum bicolor

Phospholipase C (PLC) is an essential enzyme involved in lipid signaling pathways crucial for regulating plant growth and responding to environmental stress. In sorghum, 11 PLC genes have been identified, comprising 6 PI-PLCs and 5 NPCs. Through phylogenetic and interspecies collinearity analyses, structural similarities between SbPLCs and ZmPLCs proteins have been observed, with a particularly strong collinearity between SbPLCs and OsPLCs. Promoter function analysis has shown that SbPLCs are significantly enriched under abiotic stress and hormonal stimuli, like ABA, jasmonic acid, drought, high temperature, and salt. Gene co-expression networks, constructed using a weighted gene co-expression network analysis (WGCNA), highlight distinct expression patterns of SbPLC1, SbPLC3a, and SbPLC4 in response to abiotic stress, providing further insights into the expression patterns and interactions of SbPLCs under various environmental stimuli. qRT-PCR results reveal variations in expression levels among most SbPLCs members under different stress conditions (drought, NaCl, NaHCO3), hormone treatments (ABA), and developmental stages, indicating both specific and overlapping expression patterns. This comprehensive analysis offers valuable insights into the roles of SbPLCs in sorghum, shedding light on their specific expression patterns, regulatory elements, and protein interactions across different environmental stimuli and developmental stages.

Particle size and band gap evaluation of green gold nanoparticles (AuNPs) with potential applications

Abstract The present study was aimed towards green synthesis of gold nanoparticles (AuNPs) using fungal strain (SGSK-7) with assessment of their size using different techniques viz., X-ray diffractormeter, Dynamic light scattering, Atomic force microscopy, FE-Scanning Electron Microscopy and Fourier transform Infrared Spectroscopy. The intense characteristic diffraction peaks at angle 2Ѳ (38.13˚) presented the crystalline nature of the reduced gold solution and calculation of crystalline size (12 nm) using Scherer’s equation further confirmed synthesis of gold nanoparticles while dynamic light scattering analysis indicated the particle size range of gold nanoparticles between 2 nm to 50 nm. Field Emission Scanning Electron Microscopic (FESEM) and Atomic Force Microscopy (AFM) analysis of extracellular gold nanoparticles depicts spherical shape of AuNPs of approximately 40 nm. Fourier transform Infrared (FTIR) Spectroscopy depicted the presence of the gold nanoparticles along with the other biomolecules secreted by fungus which plays vital role in reduction, capping and stabilization of gold nanoparticles. Energy dispersive X-ray, mapping analysis, Zeta potential and UV-Vis spectrophotometery analysis further confirmed the presence and stability of gold nanoparticles, respectively. Zeta potential of gold nanoparticles leads to conclude the neutral nature (-10 mV to 10mV) of the particles. The UV-Visible spectrophotometeric analysis also confirmed the formation of gold nanoparticles with an absorption peak at 547 nm. On the basis of UV-Visible spectra the optical band gap of 2.44 eV is examined. The phylogenetic relatedness of SGSK-7 revealed 99% homology with Aspergillus tamari after sequencing of the ITS region followed by BLAST.

Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.

The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits. We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops. Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the "Triangle of U" species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light. The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.

Genome-wide analysis of the SWEET gene family and its response to powdery mildew and leaf spot infection in the common oat (Avena sativa L.)

The nutritional quality and yield of oats (Avena sativa) are often compromised by plant diseases such as red leaf, powdery mildew, and leaf spot. Sugars Will Eventually be Exported Transporters (SWEETs) are newly identified sugar transporters involved in regulating plant growth and stress responses. However, the roles of SWEET genes in biotic stress responses remain uncharacterized in oats. In this study, 13 AsSWEET genes were identified across nine chromosomes of the oat genome, all of which were predicted to contain seven transmembrane regions. Phylogenetic analysis revealed four clades of AsSWEET proteins, with high homology to SWEET proteins in the Poaceae family. Collinearity analysis demonstrated strong relationships between oat and Zea mays SWEETs. Using subcellular localization prediction tools, AsSWEET proteins were predicted to localize to the plasma membrane. Promoter analysis revealed cis-acting elements associated with light response, growth, and stress regulation. Six AsSWEET proteins were predicted to interact in a network centered on AsSWEET1a and AsSWEET11. Gene expression analysis of two oat varieties, ‘ForagePlus’ and ‘Molasses’, indicated significant expression differences in several AsSWEET genes following infection with powdery mildew or leaf spot, including AsSWEET1a, AsSWEET1b, AsSWEET2b, AsSWEET3a, AsSWEET11, and AsSWEET16. These SWEET genes are potential candidates for disease resistance in oats. This study provides a foundation for understanding the regulatory mechanisms of AsSWEET genes, particularly in response to powdery mildew and leaf spot, and offers insights for enhancing oat molecular breeding.

Phylogenetic analysis of endemic Sideritis L. spp. (Lamiaceae) in Türkiye based on chloroplast trnL-F, matK, and rbcL DNA sequences

Phylogenetic analysis of endemic Sideritis L. spp. (Lamiaceae) in Türkiye based on chloroplast trnL-F, matK, and rbcL DNA sequences

Fusarium and Neocosmospora Species Associated with the Decline of Metasequoia glyptostroboides in China.

During surveys conducted in 2020, severe symptoms associated with death and decline were observed on >30-year-old Metasequoia glyptostroboides (Chinese redwood) trees in the shelter-forests along Yangtze River in Jingzhou city, Hubei province, China. A previous study showed that Phytophthora acerina was one of the causal agents of the decline of the Chinese redwood. In this study, a total of 147 fungal isolates were obtained from the diseased roots and xylem of trunks of declining M. glyptostroboides trees. Through morphology and multi-locus phylogenetic analysis, these isolates were identified as eight species belonging to the genera Fusarium and Neocosmospora including F. fujikuroi, F. irregulare, F. odoratissimum, F. reticulatum， N. falciformis, N. keratoplastica, N. solani, and N. tonkinensis. Single inoculation and co-inoculation with P. acerina assays of these Fusarium and Neocosmospora species were then performed to test pathogenicity on three-year-old seedlings of M. glyptostroboides. Lesions (i.e., on seedling stems) caused by species of the genera Neocosmopora and Fusarium were smaller than those caused by P. acerina. Co-inoculation of F. fujikuroi and P. acerina, as well as the co-inoculation of F. reticulatum and P. acerina caused larger lesions than inoculations with P. acerina alone. All these species of Fusarium and Neocosmospora were shown to have the potential to be pathogenic to M. glyptostroboides. This study provided evidence that the decline of M. glyptostroboides in Jingzhou is a disease complex.

First report of Exserohilum turcicum causing leaf blight on sudangrass (Sorghum × drummondii) in Mexico

In February 2021, elongated grey lesions with reddish margin were observed on sudangrass (Sorghum × drummondii) leaves, in the municipality of Guasave, Sinaloa, Mexico. These symptoms resembled those of leaf blight caused by Bipolaris and Exserohilum on other grasses. Two fungal isolates were recovered from symptomatic leaves, and their identities were confirmed based on a polyphasic approach. The morphological and phylogenetic analysis of the actin gene (act) and internal transcribed spacer region (ITS) of both isolates revealed their identity as Exserohilum turcicum. A pathogenicity test with a representative isolate confirmed this fungus as the causal agent of leaf blight on sudangrass, as symptoms previously observed in the field were developed on the inoculated plants. The E. turcicum isolate was recovered from the diseased sudangrass plants, fulfilling Koch’s postulates. This is the first report of E. turcicum causing leaf blight on sudangrass in Mexico.

Phylogeny, biogeography and morphological evolution of the treehopper‐like leafhoppers (Hemiptera: Cicadellidae) Megophthalminae and Ulopinae

AbstractRecent phylogenetic analyses of anchored‐hybrid, transcriptomic and morphological data have consistently recovered a clade comprising the three previously recognized families of treehoppers (Hemiptera), Aetalionidae, Melizoderidae and Membracidae, as well as two groups traditionally included in the leafhopper family Cicadellidae as subfamilies Megophthalminae and Ulopinae. To reconstruct the phylogeny of these two groups of treehopper‐like leafhoppers, maximum likelihood and multi‐species coalescent analyses were performed on a molecular DNA dataset consisting of ~700 anchored hybrid loci representing 84 terminal taxa. Analyses based on different dataset subsets and approaches yielded largely congruent topologies, although the relationships among Megophthalminae, Ulopinae and treehoppers are still unstable. The monophyly of both subfamilies is strongly supported, but several tribes, including Agalliini, Cephalelini, Megophthalmini and Ulopini, are recovered as non‐monophyletic. The origin of Megophthalminae and Ulopinae was estimated as early Cretaceous (~140 million years ago), and the divergence within each subfamily began in the mid‐Cretaceous. Continental‐scale biogeographic structure is evident in these two groups, with genera occurring on the same continent tending to group together regardless of tribal placement, suggesting that extensive morphological convergence occurred among faunas inhabiting different regions. Ancestral microhabitat reconstruction suggested that megophthalmine and ulopine leafhoppers originally lived on trees or shrubs and later several groups evolved independently to inhabit leaf litter and soil. Convergent modifications of the ocelli, forewings and hindwings accompanied changes in microhabitat preference.

A new agaricoid species of Porotheleum (Porotheleaceae, Agaricales) from Shandong Province, China

Porotheleum microsporum, a new agaricoid species of the genus Porotheleum (Porotheleaceae, Agaricales), was found growing on the live bark of Salix babylonica in Quancheng Park (Ji’nan City, Shangdong Province, China). This discovery, a testament to our rigorous research, is described and illustrated based on morphological, molecular, and ecological evidence. Our phylogenetic analyses based on DNA sequences of the internal transcribed spacers 1 and 2 with the 5.8S rDNA (ITS) and the large subunit of nuclear ribosomal DNA (LSU) support the inclusion of this new species in the genus Porotheleum as it forms an independent clade in the phylogenetic tree. Morphologically, P. microsporum differs from any known species by combining a pale-yellow pileus with an ochre-yellow center and relatively small basidiospores.

Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays.

Lettuce (Lactuca sativa L.) is a source of beneficial compounds though they are generally present in low quantities. We used 40K Axiom and 9K Infinium SNP (single nucleotide polymorphism) arrays to (i) explore the genetic variability in 21 varieties and (ii) carry out genome-wide association studies (GWAS) of vitamin C content in21 varieties and a population of 205 plants from the richest variety in vitamin C ('Lechuga del Pirineo'). Structure and phylogenetic analyses showed that the group formed mainly by traditional varieties was the most diverse, whereas the red commercial varieties clustered together and very distinguishably apart from the rest. GWAS consistently detected, in a region of chromosome 2, several SNPs related to dehydroascorbic acid (a form of vitamin C) content using three different methods to assess population structure, subpopulation membership coefficients, multidimensional scaling, and principal component analysis. The latter detected the highest number of SNPs (17) and the most significantly associated, 12 of them showing a high linkage disequilibrium with the lead SNP. Among the 84 genes in the region, some have been reported to be related to vitamin C content or antioxidant status in other crops either directly, like those encoding long non-coding RNA, several F-box proteins, and a pectinesterase/pectinesterase inhibitor, or indirectly, like extensin-1-like protein and endoglucanase 2 genes. The involvement of other genes identified within the region in vitamin C levels needs to be further studied. Understanding the genetic control of such an important quality trait in lettuce becomes very relevant from a breeding perspective.

Evolution of the pheV-tRNA integrated genomic island in Escherichia coli.

Escherichia coli exhibit extensive genetic diversity at the genome level, particularly within their accessory genome. The tRNA integrated genomic islands (GIs), a part of the E. coli accessory genome, play an important role in pathogenicity. However, studies examining the evolution of GIs have been challenging due to their large size, considerable gene content variation and fragmented assembly in draft genomes. Here we examined the evolution of the GI integrated at pheV-tRNA (GI-pheV), with a primary focus on uropathogenic E. coli (UPEC) and the globally disseminated multidrug resistant ST131 clone. We show the gene content of GI-pheV is highly diverse and arranged in a modular configuration, with the P4 integrase encoding gene intP4 the only conserved gene. Despite this diversity, the GI-pheV gene content displayed conserved features among strains from the same pathotype. In ST131, GI-pheV corresponding to the reference strain EC958 (EC958_GI-pheV) was found in ~90% of strains. Phylogenetic analyses suggested that GI-pheV in ST131 has evolved together with the core genome, with the loss/gain of specific modules (or the entire GI) linked to strain specific events. Overall, we show GI-pheV exhibits a dynamic evolutionary pathway, in which modules and genes have evolved through multiple events including insertions, deletions and recombination.

Patterns and Drivers of Pollen Temperature Tolerance.

Pollen, a pivotal stage in the plant reproductive cycle, is highly sensitive to temperature fluctuations, impacting seed quality and quantity. While the importance of understanding pollen temperature limits (Tmin, Topt, Tmax - collectively PTLs) is recognized, a comprehensive synthesis of underlying drivers is lacking. Here, we examined PTLs, correlating them with vegetative tissue thermotolerance and assessing variability at the intra- and interspecific levels across 191 species with contrasting phylogeny, cultivation history, growth form and ecology. At the species level, the PTLs range from 9.0 to 42.4°C, with considerable differences among individual species. Vegetative tissue showed greater tolerance to both low and high temperatures than pollen. A significant, though weak, correlation was observed between PTLs and leaf temperature tolerance. Pollen heat tolerance was independent of that in leaves and stems. The greatest intraspecific variability was observed in pollen cold tolerance (Tmin), followed by Topt and Tmax. Phylogenetic analysis revealed family-level conservation in all three pollen temperature tolerance measures. Climate emerged as a significant PTL driver of pollen cold tolerance, with species from colder and stable climates exhibiting enhanced cold tolerance. Cultivated and wild species did not differ in their pollen temperature tolerances. Herbaceous plants showed higher tolerance to high temperatures compared to shrubs and trees, potentially reflecting divergent thermal conditions during anthesis. This study provides the first formal analysis of complex relationships between pollen temperature limits, plant characteristics and environmental factors, providing crucial insights into climate change impacts on plant reproduction.

New records of three Basidiomycetous species from Iraq using phenotypic and phylogenetic analyses

Wild macrofungi have potential functions in ecosystems and sustainable developments through their roles in waste management, human health and societal upliftment. However, there is limited knowledge of wild macrofungi in Iraq. Three interesting collections within Chlorophyllum, Mycenastrum and Ossicaulis genera related to basidiomycetes were discovered in central and northeastern parts of Iraq in 2022 during a field investigation on wild macrofungi. Molecular identification and morphological characterization were carried out for these collections. The molecular phylogenetic and phenotypic analyses confirmed that isolates are related to three species within two families )Agaricaceae and Lyophyllaceae) belonging to the order Agaricales and class Agaricomycetes. Based on the current publications, these species were the first records from Iraq. Chlorophyllum agaricoides, Mycenastrum corium and Ossicaulis salomii sequences were submitted as the first sequences from Iraq into the international biological database GenBank. The molecular phylogenetic tree formed three independent lineages in each genus with high support. The introduced species can easily be separated from closely related species in an evolutionary framework. The study's results might aid in further investigations into the macrofungi in Iraq.

New insights into the phylogenetic relationships within the Lauraceae from mitogenomes

BackgroundThe family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences.ResultsThe mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present.ConclusionsThe topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day.

Phylogenetic and divergence analysis of Pentatomidae, with a comparison of the mitochondrial genomes of two related species (Hemiptera, Pentatomidae).

Pentatomidae, the most diverse family of Pentatomoidea, is found worldwide. Currently, the phylogenetic relationships among Pentatomidae tribes remain unstable, and subfamily divergence has not been estimated. Here, we sequenced and analyzed the complete mitochondrial genomes of two species of Lelia, and studied the phylogenetic relationships among Pentatominae tribes. We also selected three available fossil as the calibration points in the family, and preliminarily discussed the divergence time of Pentatomidae. Trees of Pentatomidae were reconstructed using the Bayesian inference method. Divergence times of Pentatominae were estimated based on the nucleotide sequences of protein-coding genes with a relaxed clock log-normal model in BEASTv.1.8.2. The results showed that the gene arrangements, nucleotide composition, and codon preferences were highly conserved in Lelia. Further, a phylogenetic analysis recovered Eysarcorini, Strachiini, Phyllocephalini, and Menidini as monophyletic with strong support, however, the monophyly of Antestiini, Nezarini, Carpocorini, Pentatomini and Cappaeini were rejected. Moreover, Pentatominae diverged from Pentatomidae soon after the origin of the Cretaceous Period, at approximately 110.38 Ma. This study enriches the mitochondrial genome database of Pentatomidae and provides a reference for further phylogenetic studies, and provides a more accurate estimate of divergence time.

A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species

Background Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation of the genus.ResultsThis study utilized genome survey of G. forrestii generated approximately 54.56 GB of sequence data, with approximately 112 × coverage. K-mer analysis indicated a genome size of approximately 0.48 GB, smaller than 0.52GB estimated by flow cytometry. The heterozygosity is of about 0.54%, and a repeat rate of around 51.54%. All the shotgun data were assembled into 339,729 scaffolds, with an N50 of 17,344 bp. The average content of guanine and cytosine was approximately 35.16%. A total of 330,999 SSRs were detected, with mononucleotide repeats being the most abundant at 70.16%, followed by dinucleotide repeats at 20.40%. We conducted a preliminary ploidy assessment using Smudgeplot and observed a clear bimodal distribution in G. forrestii at 1/2 relative coverage depth and total coverage depth (2n), suggesting a potential diploid genome structure. A pseudo chromosome of G. forrestii and a gemone of Boswellia sacra were used as reference genome to perform a primer population resequencing analysis within three Garuga species. Principal component analysis (PCA) indicated three distinct groups, but genome wide phylogenetics represented conflicting both between the dataset of different reference genomes and between maternal and nuclear genome.ConclusionIn summary, the genome of G. forrestii is small, and the phylogenetic relationships within the Garuga genus are complex. The genetic data presented in this study holds significant value for comprehensive whole-genome analyses, the evaluation of population genetic diversity, investigations into adaptive evolution, the advancement of artificial breeding efforts, and the support of species conservation and restoration initiatives. Ultimately, this research contributes to reinforcing the conservation and management of natural ecosystems, promoting biodiversity conservation, and advancing sustainable development.