Gene Expansion Research Articles

Tissue-specific, temporal, and core gene-dependent expression patterns of Hsp70s reveal functional allocation in Chlamys farreri under heat stress

Heat shock proteins 70 KDa (Hsp70s) engage in a broad spectrum of cellular functions in response to various stressors. Marine bivalves face substantial threats from the rising seawater temperature attributed to global warming. In the present study, expression patterns of Hsp70s in Zhikong scallop Chlamys farreri (CfHsp70s) were determined in embryos and larvae at all developmental stages, in healthy adult tissues, and across four various tissues exposed to high temperature for acute and chronic periods through in silico analysis. Spatiotemporal expressions suggested CfHsp70s performed specific functional differentiations in scallop's development and growth. Regulatory expression patterns of CfHsp70s, characterized by predominant down-regulation in the mantle, gill and hemocytes, as well as contrasting up-regulation in the heart, suggest differential functional allocation of CfHsp70s among tissues in response to heat stress. Particularly, a core set of 14 CfHsp70s, especially the nine members of the Hsp70B2s, characterized by gene expansion, intron-less structure, shorter gene length, preference for hydrophilic amino acids, and coordinated expression profiles, was predominantly responsible for the inducible up-regulations observed across all four tissue types. Collectively, the tissue-specific, temporal and core gene-dependent expression patterns of CfHsp70s illustrate the functional allocation and molecular evolution of Hsp70 family members in Zhikong scallops.

Comprehensive identification of LEA protein family genes and functional analysis of MdLEA60 involved in abiotic stress responses in apple (Malus domestica).

Late embryogenesis abundant (LEA) proteins are important proteins that exists widely in many plants and contribute to physiological processes of plant stress resistance. Despite LEA proteins being identified in many plants, none have been reported in apple (Malus domestica) until this study. In this study, a total of 87 MdLEA proteins were identified in apple, and a comprehensive analysis was conducted to elucidate the functions of MdLEA proteins in response to abiotic stress. Results showed that they were classified into 7 groups and distributed on 16 chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of MdLEA genes. The MdLEA promoters were enriched with elements associated with various stress responses. Through transcriptome and qRT-PCR analysis, several MdLEA genes related to drought/salinity/cold were excavated, and MdLEA60 was selected for transgenic validation. The ectopic expression of MdLEA60 enhanced osmotic and extreme temperature tolerance in both prokaryotic and eukaryotic cells, providing stress resistance support via antioxidant protection. Overall, the comprehensive analyses and identification not only establish a basis for future investigation into the functional mechanism of MdLEA proteins but also provide potential candidate genes for apple resistance breeding optimization.

Evolution of thaumatin-like proteins in rosaceae and rapid response to cold stimulation coordinated with PmEOBⅡ in the floral scent formation process of Prunus mume

Prunus mume has a long history of cultivation in China as the ornamental plant. It has been observed for a long time that the colder weather the weather appear, the sweeter the flowers produce, coldness stress may contribute to the formation of its floral scents. Here, in previous transcription matrix during scent formation period, we recognized thaumatin-like proteins from the core co-expression members. Thus, we performed the identification of thaumatin-like proteins in the Rosaceae genomes, characterized by conserved cysteine residues and tag sequences to explain the relationship between abiotic stress and floral metabolism. The numbers of TLPs ranged from 22 to 34. Most of the TLP members in Group 9 displayed congregated and expanded. A total of seven tandem duplication events occurred in 27 PmTLPs, which could be the primary driving force behind PmTLP gene expansion. The promoters of the PmTLPs contained various types of cis-elements. Additionally, there existed several miRNAs for certain PmTLPs. As a result, PmTLPs displayed tissue-specific expression trends, and expressions varied across different developmental stages of flowers. For highly activated members, PmTLP19 and 23 increased sharply after 4 h under chilling induction compared with a slow increase by ABA treatment. PmTLPs, PmEOBII, and PmMYB4 owned a positive expression correlation in both responces. Finally, the yeast two-hybrid results also indicated a strong interaction between PmEOBII and PmTLP19. Our results establish the foundation for a comprehensive investigation into the molecular mechanism of PmTLPs involved in the cold-resistant defense response of Prunus mume. Additionally, it will facilitate the identification of genes associated with regulating floral compounds in P. mume.

Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira.

The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species.

Comparative analysis of IRE1s in plants: insights into heat stress adaptation in Triticum aestivum.

The unfolded protein response (UPR) pathway serves as a crucial mechanism enabling plants to perceive, respond to, and shield themselves from adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1) is one of the key players of the UPR, and resides in the endoplasmic reticulum (ER) within the cell. This study provides a comprehensive analysis of 195 IRE1 genes across 90 diverse plant species, with a focus on their identification and characterization. To decipher the functions of IRE1 family members, we investigated the evolution and spread of IREs in plants and analysed their structural and localization characteristics. Our detailed cis-element analysis revealed unique IRE1 regulation patterns in different plant species. Furthermore, gene expression analysis revealed tissue-specific and heat stress-responsive expression patterns of TaIRE1s, which were subsequently confirmed via quantitative gene expression analysis. TaIRE1-6A was upregulated in response to dithiothreitol (DTT) treatment as well as heat stress. This finding suggests that IRE1 might play a role in linking the UPR pathway and the heat stress response (HSR). Our findings provide a comprehensive understanding of the evolution and expansion of IRE1 genes in different plant species. These findings provide a foundation for further in-depth research on the functional diversity of IREs in nutritious crops following polyploidization. By linking the UPR with HSR, IRE1 could be a key contributor to wheat's resilience against heat stress. Additionally, this connection offers important insights for future functional studies in other crops. Thus, this knowledge could be used for engineering climate resilience in crops such as wheat.

A newborn F-box gene blocks gene flow by selectively degrading phosphoglucomutase in species hybrids

The establishment of reproductive barriers such as postzygotic hybrid incompatibility (HI) remains the key to speciation. Gene duplication followed by differential functionalization has long been proposed as a major model underlying HI, but little supporting evidence exists. Here, we demonstrate that a newborn F-box gene, Cni-neib-1, of the nematode Caenorhabditis nigoni specifically inactivates an essential phosphoglucomutase encoded by Cbr-shls-1 in its sister species Caenorhabditis briggsae and their hybrids. Zygotic expression of Cni-neib-1 specifically depletes Cbr-SHLS-1, but not Cni-SHLS-1, in approximately 40 min starting from gastrulation, causing embryonic death. Cni-neib-1 is one of thirty-three paralogues emerging from a recent surge in F-box gene duplication events within C. nigoni, all of which are evolving under positive selection. Cni-neib-1 undergoes turnover even among C. nigoni populations. Differential expansion of F-box genes between the two species could reflect their distinctive innate immune responses. Collectively, we demonstrate how recent duplication of genes involved in protein degradation can cause incidental destruction of targets in hybrids that leads to HI, providing an invaluable insight into mechanisms of speciation.

Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis

Asparagales, the largest monocot order, is renowned for its ecological, economic, and medicinal significance. Here, we leverage transcriptome data from 455 Asparagales species to explore the phylogeny of Asparagales. Moreover, we investigate the evolutionary patterns of the genes involved in allium flavor formation. We not only establish a robust bifurcating phylogeny of Asparagales but also explore their reticulate relationships. Notably, we find that eight genes involved in the biosynthesis of allium flavor compounds underwent expansion in Allium species. Furthermore, we observe Allium-specific mutations in one amino acid within alliinase and three within lachrymatory factor synthase. Overall, our findings highlight the role of gene expansion, increased expression, and amino acid mutations in driving the evolution of Allium-specific compounds. These insights not only deepen our understanding of the phylogeny of Asparagales but also illuminate the genetic mechanisms underpinning specialized compounds.

Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire

BackgroundThe Nakaseomyces clade is formed by at least nine described species among which three can be pathogenic to humans, namely Nakaseomyces glabratus (Candida glabrata), the second most-common cause of candidiasis worldwide, and two rarer emerging pathogens: Nakaseomyces (Candida) nivarensis and Nakaseomyces (Candida) bracarensis. Early comparative genomics analyses identified parallel expansions of subtelomeric adhesin genes in N. glabratus and N. nivarensis/bracarensis, and suggested possible links with the emergence of the virulence potential in these species. However, as shown for N. glabratus, the proper assessment of subtelomeric genes is hindered by the use of incomplete assemblies and reliance on a single isolate.ResultsHere we sequenced seven N. bracarensis isolates and reconstructed chromosome level assemblies of two divergent strains. We show that N. bracarensis isolates belong to two diverging clades that have slightly different genomic structures. We identified the set of encoded adhesins in the two complete assemblies, and uncovered the presence of a novel adhesin motif, found mainly in N. bracarensis. Our analysis revealed a larger adhesin content in N. bracarensis than previously reported, and similar in size to that of N. glabratus. We confirm the independent adhesin expansion in these two species, which could relate to their different levels of virulence.ConclusionN. bracarensis clinical isolates belong to at least two differentiated clades. We describe a novel repeat motif found in N. bracarensis adhesins, which helps in their identification. Adhesins underwent independent expansions in N. glabratus and N. bracarensis, leading to repertoires that are qualitatively different but quantitatively similar. Given that adhesins are considered virulence factors, some of the observed differences could contribute to variations in virulence capabilities between N. glabratus and N. bracarensis.

Chromosome-scale assembly and analysis of yellow Camellia (Camellia limonia) genome reveal plant adaptation mechanism and flavonoid biosynthesis in karst region

Yellow Camellia is an endangered and protected wild plant with unique medicinal value. Among the Camellia Sect. Chrysantha Chang, certain species (e.g. Camellia limonia) can grow in karst regions. The karst region is a highly sensitive ecosystem with low environmental capacity. However, the molecular mechanisms underlying the adaptation of yellow camellia to karst regions remain unclear. Here, we present a high-quality genome with 15 chromosome groups with an N50 of 198.92 Mb. The divergence between C. limonia and Camellia sinensis occurred approximately 6 million years ago, indicating that the Himalayan uplift event may led to species differentiation. This enables C. limonia to thrive in a unique ecological environment like the karst region. Flavonoid compounds play a significant role in the interaction between plants and their environment. In comparison to Theaceae family genomes, C. limonia exhibits an increased number of gene family members involved in the flavonoid biosynthesis pathway, including UDP-glycosyltransferases and chalcone reductase. Additionally, two gene clusters associated with flavonoid biosynthesis were identified in the genome of C. limonia. Furthermore, comparative genomics analysis revealed the expansion of genes associated with karst environment adaptation in the genome of C. limonia, such as calmodulin genes and genes related to Calcium ion transmembrane transport. Additionally, at the gene expression level, it was observed that the secondary metabolism-related genes may be involved in the calcium tolerance of C. limonia. These findings provide important insights into the evolution of C. limonia, offering references for the study of plants in karst areas.

Water fluxes and nutrient absorption along the midgut of three hemipterans, Mahanarva fimbriolata, Dysdercus peruvianus, and Rhodnius prolixus

Hemiptera Order comprises insect species adapted to different diets regarding water and nutrient content and availability, thus suggesting different combinations of proteins to ensure their absorption. To find out whether hemipterans use the same or distinct set of proteins and whether these differences are related to the phylogeny or the diet, RNAseq analyses were conducted in gut sections of three hemipterans, M. fimbriolata, D. peruvianus, and R. prolixus, with remarkable distinct diet. Since only a few of the selected proteins were functionally characterized, the coded putative proteins were manually curated by bioinformatics to infer their physiological function. The results suggest a relationship between gene expression patterns and water and nutrient dietary content and availability. In contrast, putative gene expansions and deletions are related to phylogeny, corresponding to evolutionary adaptations of ancestral forms to feed on xylem, cotton seeds, and blood, resulting in more resemblances between D. peruvianus and R. prolixus than M. fimbriolata. M. fimbriolata absorbs water through aquaporins Drip and Prip in the filtration chamber by passive diffusion, with a higher contribution of water-selective Drip. D. peruvianus water absorption involves Drip and Prip, but Prip contribution appears to be higher, and they probably cooperate with water-ion cotransporters in the posterior midgut. R. prolixus absorbs water in the anterior midgut involving a sodium transporter and a putative water-urea Prip. Sugars, amino acids, and lipids might be absorbed along the midgut in the three species, with a higher contribution of the posterior midgut for amino acid and lipid absorption in M. fimbriolata and D. peruvianus and the middle midgut in R. prolixus.

Genome-Wide Analysis of HECT E3 Ligases Members in Phyllostachys edulis Provides Insights into the Role of PeHECT1 in Plant Abiotic Stress Response

Homology to E6-AP Carboxy Terminus (HECT) E3 ubiquitin ligases play pivotal roles in plant growth, development, and responses to abiotic stresses. However, the function of HECT genes in Phyllostachys edulis (P. edulis) remains largely uninvestigated. In this study, a comprehensive genome-wide analysis of the HECT E3 ubiquitin ligases gene family in P. edulis was conducted, aiming to elucidate its evolutionary relationships and gene expansion. Analysis of gene structure, conserved motifs and domains, and synteny genome regions were performed. Furthermore, cis-elements in HECT gene promoters that respond to plant hormones and environmental stresses were identified and corroborated by expression data from diverse abiotic stress conditions and hormone treatments. Based on the co-expression network of PeHECTs under cold and dehydration stresses, PeHECT1 was identified as a key candidate gene associated with abiotic stress tolerance. Overexpression of PeHECT1 in tobacco leaves significantly upregulated genes related to reactive oxygen species (ROS) detoxification and polyamine biosynthesis. Yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), and dual-luciferase (dual-LUC) assays suggested that the transcription factor ETHYLENE RESPONSE FACTOR 3 (PeERF3) bound to the dehydration-responsive element (DRE) of the promoter of PeHECT1 and activated its transcription activity. Phylogenetic analysis indicated that PeHECT1 in P. edulis exhibited a close association with the diploid herbaceous bamboo Olyra latifolia, followed by the divergence of rice and bamboo. In summary, this study enhances our comprehensive understanding of the HECT E3 ubiquitin ligases gene family in P. edulis and highlights the potential role of PeHECT1 in plant abiotic stress response.

Gene expansion in the hawkmoth Manduca sexta drives evolution of food-associated odorant receptors

Gene expansion in the hawkmoth Manduca sexta drives evolution of food-associated odorant receptors

Characterization of Cytoskeletal Profilin Genes in Plasticity Elongation of Mesocotyl and Coleoptile of Maize Under Diverse Abiotic Stresses.

The plasticity elongation of mesocotyl (MES) and coleoptile (COL) largely determines the morphology of maize seedlings under abiotic stresses. The profilin (PRF) proteins play a pivotal role in cytoskeleton dynamics and plant development via regulating actin polymerization. However, little is known about whether and how the expression of the ZmPRF gene family regulates MES and COL elongation in maize under adverse abiotic stresses. Here, a total of eight ZmPRF gene members were identified in the maize genome. They were mainly located in the cytoplasm, chloroplast, and mitochondrion, and clearly divided into four classes, based on phylogenetic analysis. Segmental duplication was the main driver for the expansion of ZmPRF genes. Ka/Ks analysis indicated that most ZmPRF genes were intensely purified and selected. Promoter cis-element analysis suggested their potential roles in response to growth and development, stress adaption, hormone response, and light response. The protein-protein interaction network and two independent RNA-sequencing analyses revealed that eight ZmPRF genes and their thirty-seven interacting genes showed varied expression patterns in MES and COL of three maize genotypes under different sowing depths, 24-epibrassinolide application, and light spectral-quality treatments, of which ZmPRF3.3 was a potential core conserved gene for breeding application. Moreover, the quantitative real-time PCR (qRT-PCR) verified that the relative expression levels of most ZmPRF genes in MES and COL under above treatments were significantly correlated with the plasticity elongation of MES and COL in maize. Therefore, these results perform a comprehensive overview of the ZmPRF family and will provide valuable information for the validation of the function of ZmPRF genes in maize development under diverse abiotic stress.

Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution

Gene duplication and divergence are essential to plant evolution. The Arabidopsis type-A response regulator (ARR) family, negative regulators in cytokinin signaling, exemplifies gene expansion and differential retention. Despite extensive research, the understanding of type-A RR homologs in woody plants remains limited. In this study, the evolution history of type-A RR gene families across four rosids and one monocot has been comprehensively investigated. Focusing on Populus deltoides, a unique pair of dispersed duplicates, PdRR8 and PdFERR, is identified, and their duplication is estimated to have occurred in the common ancestor of the four rosids. The duplication remnants corresponding to PdRR8 have been retained in all rosids but the counterpart of PdFERR has been lost. In poplar, PdRR8 shows the highest expression levels in leaves, while PdFERR is specifically expressed in female floral buds. Among various external stimuli, cold strongly represses PdRR8 promoter activity, whereas 6-BA markedly inhibits that of PdFERR. Overexpression of PdRR8 in the Arabidopsis arr16arr17 double-mutant fully complements the reduced hydrotropic response. In contrast, PdFERR fails to rescue the hydrotropic defects of the mutant. Results of evolutionary, expression and functional analyses indicate that PdRR8, rather than PdFERR, is the true ortholog of the ARR16-ARR17 paralogs. Though PdRR8 and PdFERR originate from a common ancestral gene and evolve under strong negative selection, these two dispersed duplicates have exhibited differential expression and some degree of functional divergence.

Insights into Genes Encoding LEA_1 Domain-Containing Proteins in Cyperus esculentus, a Desiccation-Tolerant Tuber Plant

LEA_1 domain-containing proteins constitute a class of late-embryogenesis-abundant proteins that are highly hydrophilic and predominantly accumulate in mature seeds. Though LEA_1 proteins have been proven to be essential for seed desiccation tolerance and longevity, little information is available on their roles in non-seed storage organs. In this study, a first genome-wide characterization of the LEA_1 gene family was conducted in tigernut (Cyperus esculentus L., Cyperaceae), whose underground tubers are desiccation tolerant with a moisture content of less than 6%. Five family members identified in tigernut are comparative to four to six found in seven other Cyperaceae plants, but relatively more than three reported in Arabidopsis. Further comparison of 125 members from 29 plant species supports early divergence of the LEA_1 family into two phylogenetic groups before angiosperm radiation, and gene expansion in tigernut was contributed by whole-genome duplications occurring after the split with the eudicot clade. These two phylogenetic groups could be further divided into six orthogroups in the momocot clade, five of which are present in tigernut and the remaining one is Poaceae specific. Frequent structural variation and expression divergence of paralogs were also observed. Significantly, in contrast to seed-preferential expression of LEA_1 genes in Arabidopsis, rice, and maize, transcriptional profiling and qRT-PCR analysis revealed that CeLEA1 genes have evolved to predominantly express in tubers, exhibiting a seed desiccation-like accumulation during tuber development. Moreover, CeLEA1 transcripts in tubers were shown to be considerably more than that of their orthologs in purple nutsedge, another Cyperaceae plant producing desiccation-sensitive tubers. These results imply species-specific activation and key roles of CeLEA1 genes in the acquisition of desiccation tolerance of tigernut tubers as observed in orthodox seeds. Our findings not only improve the understanding of lineage-specific evolution of the LEA_1 family, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution.

Prochlorococcus is a diverse picocyanobacterial genus and the most abundant phototroph on Earth. Its photosynthetic diversity divides it into high-light (HL)- or low-light (LL)-adapted groups representing broad phylogenetic grades-each composed of several monophyletic clades. Here, we physiologically characterize four new Prochlorococcus strains isolated from below the deep chlorophyll maximum in the North Pacific Ocean. We combine these physiological properties with genomic analyses to explore the evolution of photosynthetic antennae and discuss potential macroevolutionary implications. The isolates belong to deeply branching low-light-adapted clades that have no other cultivated representatives and display some unusual characteristics. For example, despite its otherwise low-light-adapted physiological characteristics, strain MIT1223 has low chl b2 content similar to high-light-adapted strains. Isolate genomes revealed that each strain contains a unique arsenal of pigment biosynthesis and binding alleles that have been horizontally acquired, contributing to the observed physiological diversity. Comparative genomic analysis of all picocyanobacteria reveals that Pcb, the major pigment carrying protein in Prochlorococcus, greatly increased in copy number and diversity per genome along a branch that coincides with the loss of facultative particle attachment. Collectively, these observations support a recently developed macroevolutionary model, in which niche-constructing radiations allowed ancestral lineages of picocyanobacteria to transition from a particle-attached to planktonic lifestyle and broadly colonize the euphotic zone.IMPORTANCEThe marine cyanobacterium, Prochlorococcus, is among the Earth's most abundant organisms, and much of its genetic and physiological diversity remains uncharacterized. Although field studies help reveal the scope of diversity, cultured isolates allow us to link genomic potential to physiological processes, illuminate eco-evolutionary feedbacks, and test theories arising from comparative genomics of wild cells. Here, we report the isolation and characterization of novel low-light (LL)-adapted Prochlorococcus strains that fill in multiple evolutionary gaps. These new strains are the first cultivated representatives of the LLVII and LLVIII paraphyletic grades of Prochlorococcus, which are broadly distributed in the lower regions of the ocean euphotic zone. Each of these grades is a unique, highly diverse section of the Prochlorococcus tree that separates distinct ecological groups: the LLVII grade branches between monophyletic clades that have facultatively particle-associated and constitutively planktonic lifestyles, whereas the LLVIII grade lies along the branch that leads to all high-light (HL)-adapted clades. Characterizing strains and genomes from these grades yields insights into the large-scale evolution of Prochlorococcus. The new LLVII and LLVIII strains are adapted to growth at very low irradiance levels and possess unique light-harvesting gene signatures and pigmentation. The LLVII strains represent the most basal Prochlorococcus group with a major expansion in photosynthetic antenna genes. Furthermore, a strain from the LLVIII grade challenges the paradigm that all LL-adapted Prochlorococcus exhibit high ratios of chl b:a2. These findings provide insights into the photophysiological evolution of Prochlorococcus and redefine what it means to be a low- vs high-light-adapted Prochlorococcus cell.

Immune Checkpoint Inhibitor Therapy and Associations with Clonal Hematopoiesis

Cancer cohorts are now known to be associated with increased rates of clonal hematopoiesis (CH). We sort to characterize the hematopoietic compartment of patients with melanoma and non-small cell lung cancer (NSCLC) given our recent population level analysis reporting evolving rates of secondary leukemias. The advent of immune checkpoint blockade (ICB) has dramatically changed our understanding of cancer biology and has altered the standards of care for patients. However, the impact of ICB on hematopoietic myeloid clonal expansion remains to be determined. We studied if exposure to ICB therapy affects hematopoietic clonal architecture and if their evolution contributed to altered hematopoiesis. Blood samples from patients with melanoma and NSCLC (n = 142) demonstrated a high prevalence of CH. Serial samples (or post ICB exposure samples; n = 25) were evaluated in melanoma and NSCLC patients. Error-corrected sequencing of a targeted panel of genes recurrently mutated in CH was performed on peripheral blood genomic DNA. In serial sample analysis, we observed that mutations in DNMT3A and TET2 increased in size with longer ICB exposures in the melanoma cohort. We also noted that patients with larger size DNMT3A mutations with further post ICB clone size expansion had longer durations of ICB exposure. All serial samples in this cohort showed a statistically significant change in VAF from baseline. In the serial sample analysis of NSCLC patients, we observed similar epigenetic expansion, although not statistically significant. Our study generates a hypothesis for two important questions: (a) Can DNMT3A or TET2 CH serve as predictors of a response to ICB therapy and serve as a novel biomarker of response to ICB therapy? (b) As ICB-exposed patients continue to live longer, the myeloid clonal expansion may portend an increased risk for subsequent myeloid malignancy development. Until now, the selective pressure of ICB/T-cell activating therapies on hematopoietic stem cells were less known and we report preliminary evidence of clonal expansion in epigenetic modifier genes (also referred to as inflammatory CH genes).

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Sea cucumbers are predominant deposit feeders in benthic ecosystems, providing protective benefits to coral reefs by reducing disease prevalence. However, how they receive sufficient nutrition from seabed sediments remains poorly understood. Here, we investigate Holothuria leucospilota, an ecologically significant tropical sea cucumber, to elucidate digestive mechanisms underlying marine deposit-feeding. Genomic analysis reveals intriguing evolutionary adaptation characterized by an expansion of digestive carbohydrase genes and a contraction of digestive protease genes, suggesting specialization in digesting microalgae. Developmentally, two pivotal dietary shifts, namely, from endogenous nutrition to planktonic feeding, and from planktonic feeding to deposit feeding, induce changes in digestive tract enzyme profiles, with adults mainly expressing carbohydrases and lipases. A nuanced symbiotic relationship exists between gut microbiota and the host, namely, specific resident bacteria supply crucial enzymes for food digestion, while other bacteria are digested and provide assimilable nutrients. Our study further identifies Holothuroidea lineage-specific lysozymes that are restrictedly expressed in the intestines to support bacterial digestion. Overall, this work advances our knowledge of the evolutionary innovations in the sea cucumber digestive system which enable them to efficiently utilize nutrients from seabed sediments and promote food recycling within marine ecosystems.

Chromosome-level genome assembly of Scathophaga stercoraria provides new insights into the evolutionary adaptations of dung flies

The yellow dung fly Scathophaga stercoraria is a widely distributed species in high-altitude regions of the Northern Hemisphere. It plays important roles as a decomposer, predator, and pollinator in the ecosystem. As a staple model organism, S. stercoraria serves as a standard test species for assessing the toxicity of drug residues in livestock dung and has been the focus of numerous studies. The genetic mechanisms underlying the ecological adaptability of S. stercoraria remain poorly understood. To fill the gap, we first assembled a high-quality chromosome-level genome of S. stercoraria, resulting in a final assembly size of 549.64 Mb, with a contig N50 of 4.06 Mb, and 92.53 % of the sequence anchored to six chromosomes. Gene family analysis revealed an expansion of Toll (Toll1), GNBP3, Cyp303a1, Cyp4d14, Cyp6g1, OR67d, and yolk protein genes in the S. stercoraria genome. Transcriptome analysis indicated that most genes in the trypsin and carboxypeptidase gene families are predominantly expressed during the larval stage, whereas the α-Amylase gene family is mainly expressed during the adult stage. Additionally, PGRP-SC is highly expressed during the larval stage, OBPs are primarily expressed during the adult stage, and yolk protein genes exhibit female-biased expression. Our study not only provides a new resource for the dung flies genomic pool, but also identifies the expression patterns of key ecologically adaptative genes and gene families at the developmental stages, which provides new insights into the ecological adaptive evolution of dung flies.

Genome-wide identification of m6A-related gene family and the involvement of TdFIP37 in salt stress in wild emmer wheat.

The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.