Search Results (284)

Horizontal gene transfer (HGT), the non-Mendelian transfer of genetic material between organisms, is relatively frequent in prokaryotes, whereas its extent among eukaryotes remains unclear. Here, we raise the hypothesis of a possible cross-phylum HGT event involving 5S ribosomal DNA (rDNA). A specific type of 5S rDNA sequence from the anuran Xenopus laevis was highly similar to a 5S rDNA sequence of the genome of its flatworm parasite Protopolystoma xenopodis. A maximum likelihood analysis revealed phylogenetic incongruence between the gene tree and the species trees, as the 5S rDNA sequence from Pr. xenopodis was grouped along with the sequences from the anurans. Sequence divergence analyses of the gene region and non-transcribed spacer also agree with an HGT event from Xenopus to Pr. xenopodis. Additionally, we examined whether contamination of the Pr. xenopodis genome assembly with frog DNA could explain our findings but found no evidence to support this hypothesis. These findings highlight the possible contribution of HGT to the high diversity observed in the 5S rDNA family. Full article

MIKC-type MADS-box transcription factors constitute one of the largest gene families in plants, playing pivotal roles in regulating plant growth and development, hormone signaling transduction, and responses to biotic and abiotic stresses. However, there have been no reports on the systematic identification and characterization of MIKC-type MADS-box proteins in walnuts. In this study, we identified 52 JrMADS genes in the walnut genome and transcriptome, and categorized them into 14 subfamilies through structural domain and phylogenetic tree analysis. It was found that these genes were unevenly distributed across 16 chromosomes. Within the MIKC-type MADS-box gene family, we identified three pairs of tandem-duplicated genes and 40 pairs of segmental duplicated genes, indicating that segmental duplication was the primary mechanism of gene amplification in walnut. Ka/Ks analysis showed that the family genes have undergone purifying selection during evolutionary processes. The promoter was predicted to contain cis-acting elements related to growth, development, plant hormones, and stress response. Expression profile analysis showed that JrMADS genes have different expression patterns in various tissues and developmental stages of male and female flower buds. Notably, an ancient clade of TM8 (JrMADS43) genes was found, which is absent in Arabidopsis but present in other flowering plants. Another gene, TM6 gene (JrMADS4), belongs to the AP3 subfamily and is a clade that has diverged from tomatoes. Through qPCR analysis, we verified the differential expression of JrMADS genes at different developmental stages (MB-1/2/3 and FB-1/2/3), with JrMADS5, JrMADS8, JrMADS14, JrMADS24, JrMADS40, JrMADS46, JrMADS47, JrGA3ox1, and JrGA3ox3 showing significantly higher expression in male than in female flower buds. In summary, our results provide valuable information for further biological functions research on MIKC-type MADS-box genes in walnut, such as flower organ development, and lays a solid foundation for future studies. Full article

The mechanisms of chemoreception in fig wasps (Hymenoptera, Agaonidae) are of primary importance in their co-evolutionary relationship with the fig trees they pollinate. As the supplementary receptors to odorant receptors (ORs) and gustatory receptors (GRs) in insects, we compare the evolutionary characters of ionotropic receptors (IRs) among 25 fig wasp taxa in six genera. In total, we identified 205 IRs in 25 fig wasps, with each taxon recording from 5 to 12 IR genes. We found 189 IR genes clustered into 18 orthologous groups that can be divided into three types: IRco, antennal IRs, and divergent IRs. More IRs belong to antennal IRs in fig wasps, which can be sensitive to acids, aldehydes, polyamines, salt, amino acids, and temperature/humidity according to homology comparison. Additionally, some IR genes in fig wasps do not cluster with those of outgroup species (e.g., Drosophila melanogaster, Apis mellifera), suggesting they may represent a unique group and may have special functions in fig wasps. Divergent IRs are very few, with large sequence variation between species. Compared to ORs and GRs in fig wasps, gene sequences in most IR orthologous groups are more conserved between genera, with the lowest sequence similarity in 10 orthologous groups (including three IRco) exhibiting above 58.5%. Gene sequences are consistent with the phylogenetic relationships among fig wasps, which is the same as ORs and GRs. Strong purifying selection of IR genes was detected, as shown by the low ω values. Signatures of positive selection were detected in loci from three orthologous groups. Our results provide important molecular information for further studies on chemosensory mechanisms in fig wasps. Full article

Photosynthetic eukaryotes have shaped the Earth’s biosphere by producing oxygen and organic compounds using light energy in specialized organelles called plastids. Plastids evolved from free-living cyanobacteria ingested by heterotrophic unicellular eukaryotes. Two such independent engulfment processes, called cyanobacterial endosymbioses, have been reported. The first gave rise to primary plastids and three Archaeplastida lineages: glaucophytes, red algae, and green algae with land plants, whereas the second resulted in chromatophores in the rhizarian amoeba Paulinella. Importantly, Archaeplastidans donated their plastids to many protist groups, further spreading photosynthesis across the tree of life. To reveal complex plastid evolution, we performed comprehensive phylogenetic and molecular clock analyses using new fossil calibrations and the largest number yet of plastid-encoded proteins from 108 taxa, representing diverse photosynthetic organisms. Our results indicate that primary plastids evolved prior to 2.1–1.8 Ga, i.e., before glaucophytes diverged from other Archaeplastidans, and Paulinella chromatophores were likely before 292–266 Ma. Red and green algae were engulfed by cryptophyte and chlorarachniophyte ancestors between 1.7–1.4 Ga and 1.1–1.0 Ga, respectively; the former subsequently triggered plastid transfers to other eukaryotes. We also examined the impact of molecular clocks and calibration sets on age estimates, showing that clocks are the main source of variation. Full article

Absidia is the most species-rich genus within the family Cunninghamellaceae, with its members commonly isolated from diverse substrates, particularly rhizosphere soil. In this study, four novel Absidia species, A. irregularis sp. nov., A. multiformis sp. nov., A. ovoidospora sp. nov., and A. verticilliformis sp. nov., were discovered from soil samples collected in southern and southwestern China, using integrated morphological and molecular analyses. Phylogenetic analyses based on concatenated ITS, SSU, LSU, Act, and TEF1α sequence data reconstructed trees that strongly supported the monophyly of each of these four new taxa. Key diagnostic features include A. irregularis (closely related to A. oblongispora) exhibiting irregular colony morphology, A. multiformis (sister to A. heterospora) demonstrating polymorphic sporangiospores, A. ovoidospora (forming a clade with A. panacisoli and A. abundans) producing distinctive ovoid sporangiospores, and A. verticilliformis (next to A. edaphica) displaying verticillately branched sporangiophores. Each novel species is formally described with comprehensive documentation, including morphological descriptions, illustrations, Fungal Names registration identifiers, designated type specimens, etymological explanations, maximum growth temperatures, and taxonomic comparisons. This work constitutes the sixth instalment in a series investigating early-diverging fungal diversity in China aiming to enhance our understanding of the diversity of fungi in tropical and subtropical ecosystems in Asia. In this paper, the known species of Absidia are expanded to 71. Full article

The AT-hook motif nuclear localized (AHL) gene family encodes transcription factors pivotal in regulating plant growth, development, and responses to abiotic stimuli, including low temperature, salinity, darkness, and drought. In this study, we systematically identified 21 BpAHL genes in birch and characterized their sequence features, evolutionary relationships, and expression dynamics. Phylogenetic analysis classified BpAHLs into two clades (Clade-A and Clade-B) and three types (Type-I, -II, and -III), based on PPC domain and AT-hook motifs. Chromosomal mapping revealed an even distribution across nine chromosomes and one contig, with dispersed duplication events recognized as the major driver of BpAHL family expansion. Tissue-specific expression profiling uncovered striking divergence: Type-I BpAHLs displayed root-predominant expression, whereas Type-II/III BpAHLs were highly expressed in plant flowers and leaves. Notably, Type-II/III BpAHL genes in leaves showed distinct expression patterns in response to cold and heat stresses, while Type-I BpAHLs in roots were down-regulated under salt stress. This study provides a comprehensive phylogenomic and functional analysis of the AHLs in birch, providing insights into their roles in enhancing abiotic stress resilience in forest trees. Full article

Background: Artemisia is a large and complex genus comprising about 500 species. Currently, only a limited number of plastomes (the chloroplast genome) of Artemisia are available. Their structures have not been comparatively analyzed, and a phylogenetic backbone based on plastome-scale data is still lacking. This situation has greatly hindered our understanding of the plastome variation patterns and infra-generic relationships of the genus. Methods: We newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combining this with previously published plastomes, we comparatively analyzed their structure and constructed phylogenetic relationships using the protein-coding sequences (CDS) of plastomes. Results: Our analyses indicated that the Artemisia plastomes are conserved in terms of their structure, GC content, gene number, and order. The sequence divergence is higher in the LSC and SSC regions than in the IR regions. Three protein-coding genes and four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), and ndhG-ndhI, were highly diverse and could be chosen as candidates of DNA barcodes. Phylogenetic trees were divided into several clades, and all four main subgenera were not monophyletic. Additionally, the phylogenetic position of A. stracheyi is still controversial. Conclusions: Plastomes can provide important information for phylogenetic constructions. This study provides insights into the infra-generic relationships within Artemisia and also lays a foundation for future evolutionary studies of this genus. Full article

Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive fungal infections and comparative analyses with 13 related Trichosporon species. The three isolates yielded high-quality assemblies of 9–10 scaffolds (~21 Mb), facilitating reliable comparisons. While most species had comparable genome sizes, Trichosporon ovoides, Trichosporon coremiiforme, and Cutaneotrichosporon mucoides displayed large, fragmented genomes, suggestive of polyploidy. ANI analysis and phylogenetic trees based on ANI and single-copy orthologs supported the classification of T. austroamericanum as a distinct clade with moderate intraspecific divergence. Using the Galleria mellonella, a model for fungal pathogenicity, all T. austroamericanum strains reduced larval survival, and NIIDF 0077300 exhibited virulence comparable to T. asahii and greater than T. inkin. To explore the gene-level differences associated with pathogenicity, we performed ortholog analysis based on single-copy genes. This revealed a unique Zn(II)₂Cys₆-type transcription factor gene (OG0010545) present only in NIIDF 0077300 and T. asahii. These findings highlight the genomic diversity and infection-associated traits of T. austroamericanum, providing a framework for future functional studies. Full article

Trogopterus xanthipes (Sciuridae, Rodentia) is a medium-sized flying squirrel species in the monotypic genus Trogopterus, and is endemic to China. It is distinguishable from other squirrels by the long black hairs on the inner and outer sides at the base of the ears and numerous ridges on the crowns of the upper and lower cheek teeth. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features and successfully sequenced its mitogenome for the first time. The T. xanthipes mitogenome was conserved in number and order of genes. We analyzed codon usage patterns, evolutionary mutation rates, K2P distance, and genetic diversity of protein-coding genes. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae, and the supported subfamilies relationship as follows: ((Xerinae + Callosciurinae) + Sciurinae) + Ratufinae. The relationship within the Sciurinae clade was ((Glaucomys + Hylopetes) + ((Trogopterus+Pteromys) + Petaurista) + Sciurus). The relationship within the Callosciurinae clade was Exilisciurus + ((Tamiops + Dremomys) + ((Lariscus+Sundasciurus) + Callosciurus)). The relationship within the Xerinae clade was Sciurotamias + (Tamias + (Callospermophilus + (Marmota + (Spermophilus + (Urocitellus + (Ictidomys + Cynomys)))))). The phylogenetic position among different subfamilies of Sciuridae was consistently recovered with high support across different datasets (PCGRNA and PCG12RNA) and supported the monophyletic lineage of each genus of Sciuridae. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which was not supported by the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. Hence, our data supported a division of the Sciuridae into five subfamilies. Full article

Heat-stress resilience is vital for poultry in tropical/subtropical regions where high temperatures impair productivity. Ake chickens, as the only naked-neck chicken breed in China, exhibit robust resistance to heat stress, but this breed lacks clarity in its genetic origins. This study utilized the next-generation sequencing data from 22 chicken breeds to conduct phylogenetic and population analyses. Gene flow analysis revealed a gene migration event from Iranian naked-neck chickens and Indian local breeds to Ake chickens, and population separation estimates suggested that the naked-neck gene was introduced to China around 500–600 years ago. NJ-tree, PCA, and population structure analyses showed that Ake chickens cluster with Yunnan native breeds, which diverged only 100–200 years ago. A selective sweep in the candidate region on chromosome 3 (97.0–97.37 Mb) showed elevated genetic differentiation (F_ST) and reduced nucleotide diversity (π) compared to the genome-wide average, indicating rapid fixation of the trait under natural/artificial selection. Demographic reconstruction indicated that the current effective size of Ake chickens is stable at 2000–3000 individuals. These findings deepen our understanding of Ake chicken evolution and provide valuable insights for conservation and the development of heat-stress-resistant poultry breeds. Full article

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene–Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies. Full article

The SARS-CoV-2 virus, which causes COVID-19, has rapidly evolved, producing highly transmissible variants like Omicron. Non-structural protein 6 (NSP6) is essential for viral replication and immune evasion. This study analyzed the NSP6 protein of the Omicron variant, focusing on conserved motifs, mutations, and residual properties to better understand its structure, function, and potential for immune evasion. Sequences from humans in South America were obtained from GISAID and aligned using Clustal Omega 1.2.4, with mutations identified by a Python 3 algorithm and conserved motifs detected using the MEME tool. Sequence diversity was assessed with Shannon’s entropy, while hydrophilicity, flexibility, accessibility, and antigenicity were analyzed using EMBOSS PEPSTATS and Expasy’s ProtScale tools. Phylogenetic analysis was performed with IQ-TREE software. Analysis of 161 NSP6 protein sequences revealed significant divergence from the reference sequence, with mutations proximal to conserved regions indicating potential functional and structural changes. The analysis also identified distinct hydrophobic and hydrophilic regions, with specific amino acid positions showing high flexibility and antigenicity. Phylogenetic analysis identified three clades with varying degrees of similarity to the reference sequence. This comprehensive study of the NSP6 protein in the Omicron variant provides insights into its role in viral replication and immune evasion, contributing to the development of targeted interventions against COVID-19. Full article

The mountainous regions of Southwest China are biodiversity hotspots where geographical isolation promotes genetic differentiation and species diversification. For cave-dwelling species like the Pterocryptis anomala, how geographical isolation, historical climate, and riverscapes have influenced their evolution remains largely unexplored. Based on 255 samples from the Pearl River and the Yangtze River, this study integrated two mitochondrial genes and two nuclear genes to analyze the genetic diversity and structure of the P. anomala population. Phylogenetic trees based on mitochondrial DNA revealed two distinct clades of P. anomala, while nuclear DNA loci showed no clear separation. Spatial Analysis of Molecular Variance (SAMOVA) confirmed two groups: Clade I (the Yangtze, the Guijiang, and the Duliujiang Rivers) and Clade II (the Nanpanjiang, Hongshui, Dahuanjiang, Youjiang, and Rongjiang Rivers). The divergence time between the two clades was estimated at 13.73 million years ago, which was potentially linked to the impact of the QTP uplift on monsoonal systems. The star-like network analysis and neutrality test results indicated that the population of Clade I has maintained a stable state over a long period, while the population of Clade II showed a trend of expansion. Additionally, geographical features such as the Nanling Mountains and the two major river systems may have obstructed gene flow, leading to genetic differentiation. These findings improved our understanding of this species’ evolutionary history and population structure, offering valuable insights for conservation efforts. Full article

Scomberomorus guttatus and Scomberomorus commerson are both important marine economic fish species worldwide, with high scientific and ecological value. In this study, the complete mitochondrial genome sequences of these two species of mackerel were obtained by using next-generation sequencing technology, with total lengths of 16,562 bp and 16,594 bp, respectively. Like most teleosts, both species possess 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region D-loop. The base composition showed significant AT bias (55.1%, 53.4%) and anti-G bias (16.0%, 16.2%). In their control area, the terminal-associated sequence (TAS) was identified, and a total of three core sequences with repeated “---TACAT---ATGTA---” were found. There are typical CSB-E structures and CSB-D-like structures in the central conserved domain (CD), but no CSB-F structures have been found. Meanwhile, the CSB-2 and CSB-3 structures were identified in the conserved sequence block (CSB), but the CSB-1 structure was missing. To further investigate the phylogenetic relationships within the Scombridae family, this study conducted a comparative analysis of mitochondrial genomes from 30 Scombridae species. Phylogenetic trees encompassing 60% of the documented Scombridae species were constructed using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods. The results revealed a close evolutionary relationship between the genus Scomber and Rastrelliger, while the genus Scomberomorus exhibited closer affinities to Thunnus, Euthynnus, and Katsuwonus. At the species level, Scomberomorus guttatus diverged earlier from Scomberomorus commerson. These findings refine and update the phylogenetic relationships among Scombridae species, providing critical molecular evidence and insights for deeper exploration of their evolutionary history and genetic affinities. Full article

Understanding ecological niche evolution patterns is crucial for elucidating biogeographic history and guiding biodiversity conservation. Taxus is a Tertiary relict gymnosperm with 11 lineages mainly distributed across East Asia, spanning from tropical to subarctic regions. However, the spatiotemporal dynamics of its ecological niche evolution and the roles of ecological and geographical factors in lineage diversification, remain unclear. Using occurrence records, environmental data, and reconstructed phylogenies, we employed ensemble ecological niche models (eENMs), environmental principle components analysis (PCA-env), and phyloclimatic modeling to analyze niche similarity and evolution among 11 Taxus lineages. Based on reconstructed Bayesian trees and geographical distribution characteristics, we classified the eleven lineages into four clades: Northern (T. cuspidata), Central (T. chinensis, T. qinlingensis, and the Emei type), Western (T. wallichiana, T. florinii, and T. contorta), and Southern (T. calcicola, T. phytonii, T. mairei, and the Huangshan type). Orogenic activities and climate changes in the Tibetan Plateau since the Late Miocene likely facilitated the local adaptation of ancestral populations in Central China, the Hengduan Mountains, and the Yunnan–Guizhou Plateau, driving their expansion and diversification towards the west and south. Key environmental variables, including extreme temperature, temperature and precipitation variability, light, and altitude, were identified as major drivers of current niche divergence. Both niche conservatism and divergence were observed, with early conservatism followed by recent divergence. The Southern clade exhibits high heat and moisture tolerance, suggesting an adaptive shift, while the Central and Western clades retain ancestral drought and cold tolerance, displaying significant phylogenetic niche conservatism (PNC). We recommend prioritizing the conservation of T. qinlingensis, which exhibits the highest PNC level, particularly in the Qinling, Daba, and Taihang Mountains, which are highly degraded and vulnerable to future climate fluctuations. Full article