Divergent Gene Research Articles

The functional divergence of homologous GPAT9 genes contributes to the erucic acid content of Brassica napus seeds

BackgroundThe early allopolyploid Brassica napus was a hybrid of two Brassica species, that had undergone a whole genome duplication event followed by genome restructuring, including deletions and small scale duplications. A large number of homologous genes appeared functional divergence during species domestication. Due to the high conservation of de novo glycerolipid biosynthesis, multiple homologues of glycerol-3-phosphate acyltransferases (GPATs) have been found in B. napus. Moreover, the functional variances among these homologous GPAT-encoding genes are unclear.ResultsIn this study, four B. napus homologous genes encoding glycerol-3-phosphate acyltransferase 9 (BnaGPAT9) were characterized. Although a bioinformatics analysis indicated high protein sequence similarity, the homologues demonstrated tissue-specific expression patterns and functional divergence. Yeast genetic complementation assays revealed that BnaGPAT9-A1/C1 homologues but not BnaGPAT9-A10/C9 homologues encoded functional GPAT enzymes. Furthermore, a single nucleotide polymorphism of BnaGPAT9-C1 that occurred during the domestication process was associated with enzyme activity and contributed to the fatty acid composition. The seed-specific expression of BnGPAT9-C11124A increased the erucic acid content in the transformant seeds.ConclusionsThis study revealed that BnaGPAT9 gene homologues evolved into functionally divergent forms with important roles in erucic acid biosynthesis.

Abstract B094: The role of paraspeckles and splicing regulation in driving basal-like pancreatic cancer

Abstract The basal-like pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive type of mesenchymal PDAC that resists treatment and has a poor prognosis. Understanding the mechanisms driving basal-like PDAC biology will be essential for development of treatment strategies for this aggressive tumor. We have previously shown that loss of the tumor-suppressive non-coding RNA Neat1 recapitulate the phenotype of Arid1a-deficient mice (a component of the SWI/SNF chromatin remodeling complex) in a mouse model for PDAC, with loss of exocrine pancreatic identity and development of acinar- and ductal-derived lesions (Mello et al., 2017), suggesting that Neat1 and Arid1a may share a common molecular mechanism. We now demonstrate that the loss of these two divergent genes induce the emergence of basal-like PDAC. This provides an opportunity to probe for shared features specific to Neat1- and Arid1a-deficient PDAC, as compared to PDAC in which both genes are functional. Notably, our data indicate that both Neat1- and Arid1a-deficient pancreatic cells fail to form nuclear paraspeckles, i.e. structures implicated in the retention of RNA splicing factors. Consistent with this idea, we also find significantly increased exon-skipping, including a sub-set of such events shared between Neat1- and Arid1a-deficient PDAC. In addition, nucleotide sequence motifs associated with exon-skipping locations suggest involvement of RNA splicing factors known to accumulate in paraspeckles, such as Srsf1, Srsf2, Srsf10, Rbm38, Dazap1 and others. We also show that, upon genetic or pharmacological attenuation of splicing regulator function, basal-like PDAC develop epithelial features, reminiscent of mesenchymal-epithelial transition, reduce both their proliferation and migration potential and undergo cell death. Our findings provide an important opportunity to elucidate the molecular pathways that link aberrant RNA splicing and paraspeckle deficiency to basal-like PDAC, providing new insight for the development of mechanism-based novel PDAC treatment strategies to improve patient outcome. Citation Format: Zamira G. Soares, Emily Berry, Dakarai Esgdaille, Jennifer Twardowski, Stephano S. Mello. The role of paraspeckles and splicing regulation in driving basal-like pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B094.

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.).

MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.

Morphological and genetic analyses verify the occurrence of the butterfly Graphium chironides (Lepidoptera: Papilionidae) in Peninsular Malaysia and resolve the confusion on the validity of its subspecies malayanum Eliot, 1982

Graphium chironides malayanum Eliot, 1982 was described as a taxon occurring sympatrically with G. bathycles bathycloides in Peninsular Malaysia. However, the validity of the subspecies has been questioned in a recent publication that was based on a study of DNA and morphology, implying that G. c. malayanum is a synonym of G. b. bathycloides and G. chironides is absent from the Peninsula. A re-examination of male wing morphology, genitalia and DNA shows that G. c. malayanum is a valid taxon distinguished from G. b. bathycloides by wider discal markings, a less falcate forewing, distinct differences in the arms of the harpe in the male genitalia and clearly divergent mtDNA COI genes. In the DNA analysis, G. c. malayanum formed a monophyletic clade closely related to G. chironides from China, and both were well-separated from the G. b. bathycloides clade. An examination of characters used in the previous study showed that the conclusions reached were due to misinterpretation of diagnostic characters, misidentification of specimens and the absence of G. c. malayanum among the specimens examined. When these characters were correctly interpreted, each specimen was readily assigned to the correct taxon. Diagnostic morphological characters are reclarified based on the current data.

Effect of structural variation in the promoter region of RsMYB1.1 on the skin color of radish taproot.

Accumulation of anthocyanins in the taproot of radish is an agronomic trait beneficial for human health. Several genetic loci are related to a red skin or flesh color of radish, however, the functional divergence of candidate genes between non-red and red radishes has not been investigated. Here, we report that a novel genetic locus on the R2 chromosome, where RsMYB1.1 is located, is associated with the red color of the skin of radish taproot. A genome-wide association study (GWAS) of 66 non-red-skinned (nR) and 34 red-skinned (R) radish accessions identified three nonsynonymous single nucleotide polymorphisms (SNPs) in the third exon of RsMYB1.1. Although the genotypes of SNP loci differed between the nR and R radishes, no functional difference in the RsMYB1.1 proteins of nR and R radishes in their physical interaction with RsTT8 was detected by yeast-two hybrid assay or in anthocyanin accumulation in tobacco and radish leaves coexpressing RsMYB1.1 and RsTT8. By contrast, insertion- or deletion-based GWAS revealed that one large AT-rich low-complexity sequence of 1.3-2 kb was inserted in the promoter region of RsMYB1.1 in the nR radishes (RsMYB1.1nR), whereas the R radishes had no such insertion; this represents a presence/absence variation (PAV). This insertion sequence (RsIS) was radish specific and distributed among the nine chromosomes of Raphanus genomes. Despite the extremely low transcription level of RsMYB1.1nR in the nR radishes, the inactive RsMYB1.1nR promoter could be functionally restored by deletion of the RsIS. The results of a transient expression assay using radish root sections suggested that the RsIS negatively regulates the expression of RsMYB1.1nR, resulting in the downregulation of anthocyanin biosynthesis genes, including RsCHS, RsDFR, and RsANS, in the nR radishes. This work provides the first evidence of the involvement of PAV in an agronomic trait of radish.

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.

Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.

Comparative analysis of asian carps parvalbumin reveals the divergence pattern of major fish allergen.

Asian carps, a popular freshwater fish globally, are valued for their flavor and serve as a crucial protein source, especially for infants. However, grass carp parvalbumin is highly allergenic, surpassing the allergenicity of fish like salmon and cod. The allergenic potential of parvalbumin in other Asian carps remains unknown, underscoring the need for allergen identification to improve the precision of fish allergy diagnosis and treatment. To identify all parvalbumin homologs in Asian carps and investigate the role of gene divergence in allergenic homolog formation. Three annotated genomes of Asian carp, including grass carp, black carp and bighead carp, were constructed using a hybrid assembly approach. Through sequence homology at the genomic level, all the homologs of major fish allergens were identified. Bioinformatics tools were then employed to reveal the gene structures, expression levels, and protein conformations of parvalbumin. Grass carp genome analysis showed nine parvalbumin homologs, with Cid_PV2 most similar to Cten i 1. Bighead and black carp genomes had ten homologs, including potentially allergenic Mpi_PV7 and Hno_PV7. Tissue-specific expression patterns revealed alternative usage of parvalbumin homologs. Gene duplication events expanded parvalbumin copies in bony fish, with two gene clusters identified in Asian carp genomes. All the homologs of Asian carps' parvalbumin were accurately identified and gene divergence contributed to the formation of allergenic homologs. Together with a comprehensive gene sequence profile of carps' parvalbumin, those could be applied to achieve a more precise clinical diagnostic test.

Far-red light photoacclimation in a desert Chroococcidiopsis strain with a reduced FaRLiP gene cluster and expression of its chlorophyll f synthase in space-resistant isolates.

Some cyanobacteria can use far-red light (FRL) to drive oxygenic photosynthesis, a phenomenon known as Far-Red Light Photoacclimation (FaRLiP). It can expand photosynthetically active radiation beyond the visible light (VL) range. Therefore, it holds promise for biotechnological applications and may prove useful for the future human exploration of outer space. Typically, FaRLiP relies on a cluster of ~20 genes, encoding paralogs of the standard photosynthetic machinery. One of them, a highly divergent D1 gene known as chlF (or psbA4), is the synthase responsible for the formation of the FRL-absorbing chlorophyll f (Chl f) that is essential for FaRLiP. The minimum gene set required for this phenotype is unclear. The desert cyanobacterium Chroococcidiopsis sp. CCMEE 010 is unusual in being capable of FaRLiP with a reduced gene cluster (15 genes), and it lacks most of the genes encoding FR-Photosystem I. Here we investigated whether the reduced gene cluster of Chroococcidiopsis sp. CCMEE 010 is transcriptionally regulated by FRL and characterized the spectral changes that occur during the FaRLiP response of Chroococcidiopsis sp. CCMEE 010. In addition, the heterologous expression of the Chl f synthase from CCMEE 010 was attempted in three closely related desert strains of Chroococcidiopsis. All 15 genes of the FaRLiP cluster were preferentially expressed under FRL, accompanied by a progressive red-shift of the photosynthetic absorption spectrum. The Chl f synthase from CCMEE 010 was successfully expressed in two desert strains of Chroococcidiopsis and transformants could be selected in both VL and FRL. In Chroococcidiopsis sp. CCME 010, all the far-red genes of the unusually reduced FaRLiP cluster, are transcriptionally regulated by FRL and two closely related desert strains heterologously expressing the chlF010 gene could grow in FRL. Since the transformation hosts had been reported to survive outer space conditions, such an achievement lays the foundation toward novel cyanobacteria-based technologies to support human space exploration.

Impact of feralization on evolutionary trajectories in the genomes of feral cat island populations.

Feralization is the process of domesticated animals returning to the wild and it is considered the counterpart of domestication. Molecular genetic changes are well documented in domesticated organisms but understudied in feral populations. In this study, the genetic differentiation between domestic and feral cats was inferred by analysing whole-genome sequencing data of two geographically distant feral cat island populations, Dirk Hartog Island (Australia) and Kaho'olawe (Hawaii) as well as domestic cats and European wildcats. The study investigated population structure, genetic differentiation, genetic diversity, highly differentiated genes, and recombination rates. Genetic structure analyses linked both feral cat populations to North American domestic and European cat populations. Recombination rates in feral cats were lower than in domestic cats but higher than in wildcats. For Australian and Hawaiian feral cats, 105 and 94 highly differentiated genes compared to domestic cats respectively, were identified. Annotated genes had similar functions, with almost 30% of the divergent genes related to nervous system development in both feral groups. Twenty mutually highly differentiated genes were found in both feral populations. Evolution of highly differentiated genes was likely driven by specific demographic histories, the relaxation of the selective pressures associated with domestication, and adaptation to novel environments to a minor extent. Random drift was the prevailing force driving highly divergent regions, with relaxed selection in feral populations also playing a significant role in differentiation from domestic cats. The study demonstrates that feralization is an independent process that brings feral cats on a unique evolutionary trajectory.

Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees.

The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.

Genomic insight into the insecticidal potential of a new Pseudomonas chlororaphis isolate.

Pseudomonas fluorescens group, such as Pseudomonas protegens and Pseudomonas chlororaphis, can be utilized as insect-killing agents. Most insecticidal Pseudomonas described so far have high toxicity for insects of the order Lepidoptera. In this study, Pseudomonas strain PcR3-3 was isolated from the willow root. It showed a high mortality for the coleopteran species Plagiodera versicolora (Coleoptera: Chrysomelidae), but not for the lepidopteran Helicoverpa armigera. Strain PcR3-3 displayed high colonization ability in the P. versicolora compared with P. chlororaphis PCL1391, indicating that the insecticidal activities correlated with the colonization ability of Pseudomonas strain in the host. Phylogenetic analysis of the genome revealed that PcR3-3 belonged to P. chlororaphis subsp. aureofaciens. Numerous insecticidal protein-encoding genes, typical biosynthetic gene clusters for some insecticidal metabolite and type VI secretion system, known to be involved in insect pathogenicity, were present in the P. chlororaphis PcR3-3 genome. However, the insecticidal toxin Fit-encoding gene which commonly presents in P. chlororaphis, was not found in the P. chlororaphis PcR3-3 genome. Furthermore, there are some divergent insecticidal genes between P. chlororaphis PcR3-3 and P. chlororaphis PCL1391. This finding implies that P. chlororaphis PcR3-3 is a promising biocontrol agent for pest management applications. The P. chlororaphis-P. versicolora association can be used as a model system to study the interaction between Pseudomonas and coleopteran insects.

Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina

Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes through Müller glia (MG) reprogramming and asymmetric cell division that produces a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, do MG reprogram to a developmental retinal progenitor cell (RPC) state? Second, to what extent does regeneration recapitulate retinal development? And finally, does loss of different retinal cell subtypes induce unique MG regeneration responses? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. Here we show that injury induces MG to reprogram to a state similar to late-stage RPCs. However, there are major transcriptional differences between MGPCs and RPCs, as well as major transcriptional differences between activated MG and MGPCs when different retinal cell subtypes are damaged. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes.

Conserved and divergent gene regulatory programs of the mammalian neocortex

Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil.

The bacterial strain WB46 was isolated from the rhizosphere of willow plants (Salix purpurea L.) growing in soil contaminated with petroleum hydrocarbons. The strain was subjected to whole-genome shotgun sequencing using Illumina HiSeq. Its draft genome is 7.15 Mb, with a 69.55% GC content, containing 6387 protein-coding genes and 51 tRNA and 15 rRNA sequences. The quality and reliability of the genome were assessed using CheckM, attaining an estimated genome completeness of 98.75% and an estimated contamination of 1.68%. These results indicate a high-quality genome (>95%) and low contamination (<5%). Many of these genes are responsible for petroleum hydrocarbon degradation, such as alkane 1-monooxygenase (alkB) and naphthalene dioxygenase (ndo). 16S rRNA gene analysis, including in silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI), showed that strain WB46 belongs to the genus Nocardia, and the most closely related species is Nocardia asteroides. The strain WB46 showed a distance of 63.4% and sequence identity of 88.63%, respectively. These values fall below the threshold levels of 70% and 95%, respectively, suggesting that the strain WB46 is a new species. We propose the name of Nocardia canadensis sp. nov. for this new species. Interestingly, the sequence divergence of the 16S rRNA gene showed that the divergence only occurred in the V2 region. Therefore, the conventional V3-V4, V5-V7, or V8-V9 targeting metabarcoding, among others, would not be able to assess the diversity related to this new species.

Genome-Wide Identification, Evolution, and Expression Analysis of the MAPK Gene Family in Rosaceae Plants

Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of 97 MAPK members were identified in six Rosaceae species, including 12 genes in Fragaria vesca, 22 genes in Malus domestica, 23 genes in Pyrus bretschneideri, 12 genes in Prunus mume, 14 genes in Prunus persica, and 14 genes in Rosa chinensis. All MAPK members of six Rosaceae plants were categorized into four clusters by the phylogenetic relationship analysis. Collinearity analysis discovered that both segmental duplication and tandem duplication contributed to the expansion of MAPK family genes in Rosaceae plants. And the analysis of motifs and gene structures indicated that the evolution of the MAPK gene family was highly conserved among phylogenetic clusters in Rosaceae species. In addition, the dN/dS rates of MAPK paralogous gene pairs were below one, suggesting the MAPK gene family in Rosaceae was driven by purifying selective pressure. Furthermore, functional divergence analysis discovered that 14 amino acid residues were detected as potentially key sites for functional divergence of MAPK family genes between different cluster pairs, specifically Type I functional divergence. The analysis of functional distance indicated that cluster C retained more of the original functional features, while cluster B exhibited functional specialization. Moreover, the expression profiles revealed that PmMAPK8, PmMAPK9, and PmMAPK10 were both highly expressed under drought stress and low temperature conditions. This study aims to comprehensively analyze the evolutionary process and functional analyses of the MAPK gene family in Rosaceae plants, which will lay the foundation for future studies into MAPK genes of Rosaceae in response to drought and cold stress.

Unveiling strain-level dynamics in probiotic activity

Divergent gene content among distinct probiotic strains contributes to varied or conflicting clinical efficacies. Zhang et al. unveils a novel bacterial gene signature, particularly the abfA gene cluster, offering a promising avenue for screening probiotics and advancing our understanding of strain-level activities in the context of gastrointestinal health.

Phylogenetic Analysis of Blast Resistant RMG7 (Resistance to Magnaporthe Grisea 7) Gene in Cereals (Wheat and Rice)

Understanding the emergence and evolution of plant pathogens has benefited greatly from phylogenetic approaches. Phylogenetic analysis of the Blast Resistant RMG7 (Resistance to Magnaporthe grisea 7) gene would involve the study of its evolutionary relationships with related genes across different species. This study aimed to understand the gene's origin, divergence, and evolutionary history, which can provide insights into its function and potential applications in crop improvement. The study obtained the total of 36 DNA sequences of the RMG7 gene from different organisms (wheat and rice) from publicly available NCBI(https://www.ncbi.nlm.nih.gov) database on 20 May 2023 to investigate its evolution. The Sequences were selected based on the representation of a diverse range of species, including those known to have blast resistance or related traits. Using the generic time reversible model and the maximum likelihood method, evolutionary history was determined. These methods used statistical algorithms to estimate the evolutionary relationships between the sequences, forming a tree that represents their common ancestry. An evolutionary tree evolved using the aligned RMG7 sequences to determine the common ancestor of each strain. The Geneious software, for which purpose (sequence alignment), which tool (such as muscle, geneious aligner, cluster) was used to carry sequence alignment, including parameters (in Geneious: local alignment or global, and at which identity value (65% identical) used in doing the alignment. The phylogenetic analysis showed that the resulting tree to interpret the evolutionary relationships among the RMG7 gene sequences. The Intensified clusters or branches that group sequences with similar blast resistance characteristics or closely related species. Overall, this research provides valuable insights into the evolutionary history, genetic diversity, and relatedness of the RMG7 gene in cereals, particularly in wheat and rice. The findings have implications for understanding the mechanisms of blast resistance and for enhancing crop protection strategies against Magnaporthe grisea.

Comparative transcriptomics reveals the conservation and divergence of reproductive genes across three sympatric Tomicus bark beetles

Three tree-killing bark beetles belonging to the genus Tomicus, Tomicus yunnanensis, Tomicus brevipilosus and Tomicus minor (Coleoptera; Curculionidae, Scolytinae), are serious wood-borers with larvae feeding on the phloem tissues of Pinus yunnanensis. The three Tomicus beetles, in some cases, coexist in a same habitat, providing a best system for exploring the conservation and divergence of reproductive genes. Here, we applied comparative transcriptomics and molecular biology approaches to characterize reproductive-related genes in three sympatric Tomicus species. Illumina sequencing of female and male reproductive systems and residual bodies generated a large number of clean reads, representing 185,920,232 sequences in T. yunnanensis, 169,153,404 in T. brevipilosus and 178,493,176 in T. minor that were assembled into 32,802, 56,912 and 33,670 unigenes, respectively. The majority of the genes had detectable expression in reproductive tissues (FPKM >1), particularly those genes in T. brevipilosus accounting for 76.61 % of the total genes. From the transcriptomes, totally 838 genes encoding 463 detoxification enzymes, 339 chemosensory membrane proteins and 36 ionotropic glutamate receptors (iGluRs) were identified, including 622 reproductive tissue-expressed genes. Of these, members of carboxylesterases (COEs), ionotropic receptors (IRs), sensory neuron membrane proteins (SNMPs) and iGluRs were highly conserved in gene numbers and sequence identities across three Tomicus species. Further, expression profiling analyses revealed a number of genes expressed in reproductive tissues and the diverse expression characteristics in these beetles. The results provide evidence for the conservation and differences of reproductive genes among three sympatric closely related beetles, helping understand their different reproductive strategies and the maximization of the reproductive success.

Gene duplication and functional divergence of new genes contributed to the polar acclimation of Antarctic green algae.

The online version contains supplementary material available at 10.1007/s42995-023-00203-z.

Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae: insights from evolutionary analysis of the SOT gene family in angiosperms.

Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. While prior research has addressed gene duplications within the SOT gene family in Rosaceae, the precise origin and evolutionary dynamics of these duplications remain unclear, largely due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships among all identified Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage-specific expansion and syntenic conservation of PLTs and SOTs across diverse plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of tandemly duplicated PLT genes within Class III-A. Furthermore, our investigation highlights the role of lineage-specific and synergistic duplications in Amygdaloideae in contributing to the expansion of SOTs in Rosaceae plants. Collectively, our findings provide insights into the genomic origins, duplication events, and subsequent divergence of SOT gene family members. Such insights lay a crucial foundation for comprehensive functional characterizations in future studies.