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The genome sequencing revolution has revealed that all species possess a large number of unique genes critical for trait variation, adaptation, and evolutionary innovation. One widely used approach to identify such genes consists of detecting protein‐coding sequences with no homology in other genomes, termed orphan genes. These genes have been extensively studied, under the assumption that they represent valid proxies for species‐specific genes. Here, we critically evaluate taxonomic, phylogenetic, and sequence evolution evidence showing that orphan genes belong to a range of evolutionary ages and thus cannot be assigned to a single lineage. Furthermore, we show that the processes generating orphan genes are substantially more diverse than generally thought and include horizontal gene transfer, transposable element domestication, and overprinting. Thus, orphan genes represent a heterogeneous collection of genes rather than a single biological entity, making them unsuitable as a subject for meaningful investigation of gene evolution and phenotypic innovation. [ABSTRACT FROM AUTHOR]

The impact of global warming is increasing and thus exacerbating environmental stresses that affect plant yield and distribution, including the Eriobotrya japonica Lindl (Loquat tree). Eriobotrya japonica, a member of the Rosaceae family, is valued not only for its nutritious fruit but also for its medicinal purposes, landscape uses, and other pharmacological benefits. Nonetheless, the productivity of Eriobotrya japonica has raised a lot of concern in the wake of adverse environmental conditions. Understanding the characteristics of the LRR-RLK gene family in loquat is crucial, as these genes play vital roles in plant stress responses. In this study, 283 LRR-RLK genes were identified in the genome of E. japonica that were randomly positioned on 17 chromosomes and 24 contigs. The 283 EjLRR-RLK proteins clustered into 21 classes and subclasses in the phylogenetic analysis based on domain and protein arrangements. Further explorations in the promoter regions of the EjLRR-RLK genes showed an abundance of cis-regulatory elements that functioned in growth and development, phytohormone, and biotic and abiotic responses. Most cis-elements were present in the biotic and abiotic responses suggesting that the EjLRR-RLK genes are invested in regulating both biotic and abiotic stresses. Additional investigations into the responses of EjLRR-RLK genes to abiotic stress using the RT-qPCR revealed that EjLRR-RLK genes respond to abiotic stress, especially heat and salt stresses. Particularly, EjapXI-1.6 and EjapI-2.5 exhibited constant upregulation in all stresses analyzed, indicating that these may take an active role in regulating abiotic stresses. Our findings suggest the pivotal functions of EjLRR-RLK genes although additional research is still required. This research aims to provide useful information relating to the characterization of EjLRR-RLK genes and their responses to environmental stresses, establishing a concrete base for the following research. [ABSTRACT FROM AUTHOR]

Here we investigate the evolutionary dynamics of five enzyme superfamilies (CYPs, GSTs, UGTs, CCEs and ABCs) involved in detoxification in Helicoverpa armigera. The reference assembly for an African isolate of the major lineages, H. a. armigera, has 373 genes in the five superfamilies. Most of its CYPs, GSTs, UGTs and CCEs and a few of its ABCs occur in blocks and most of the clustered genes are in subfamilies specifically implicated in detoxification. Most of the genes have orthologues in the reference genome for the Oceania lineage, H. a. conferta. However, clustered orthologues and subfamilies specifically implicated in detoxification show greater sequence divergence and less constraint on non‐synonymous differences between the two assemblies than do other members of the five superfamilies. Two duplicated CYPs, which were found in the H. a. armigera but not H. a. conferta reference genome, were also missing in 16 Chinese populations spanning two different lineages of H. a. armigera. The enzyme produced by one of these duplicates has higher activity against esfenvalerate than a previously described chimeric CYP mutant conferring pyrethroid resistance. Various transposable elements were found in the introns of most detoxification genes, generating diverse gene structures. Extensive resequencing data for the Chinese H. a. armigera and H. a. conferta lineages also revealed complex copy number polymorphisms in 17 CCE001s in a cluster also implicated in pyrethroid metabolism, with substantial haplotype differences between all three lineages. Our results suggest that cotton bollworm has a versatile complement of detoxification genes which are evolving in diverse ways across its range. [ABSTRACT FROM AUTHOR]

For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins. [ABSTRACT FROM AUTHOR]

The Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to cancer progression. In addition to well-known hotspot mutations in RNAase III domains, DICER1 is characterized by a wide spectrum of variants in all the functional domains; most are of uncertain significance and unstated clinical effects. Moreover, various new somatic DICER1 mutations continuously appear in cancer genome sequencing. The latest contemporary methods of variant effect prediction utilize machine learning algorithms on bulk data, yielding suboptimal correlation with biological data. Consequently, such analysis should be conducted based on the functional and structural characteristics of each protein, using a well-grounded targeted dataset rather than relying on large amounts of unsupervised data. Domains are the functional and evolutionary units of a protein; the analysis of the whole protein should be based on separate and independent examinations of each domain by their evolutionary reconstruction. Dicer represents a hallmark example of a multidomain protein, and we confirmed the phylogenetic multidomain approach being beneficial for the clinical effect prediction of Dicer variants. Because Dicer was suggested to have a putative role in hematological malignancies, we examined variants of DICER1 occurring outside the well-known hotspots of the RNase III domain in this type of cancer using phylogenetic reconstruction of individual domain history. Examined substitutions might disrupt the Dicer function, which was demonstrated by molecular dynamic simulation, where distinct structural alterations were observed for each mutation. Our approach can be utilized to study other multidomain proteins and to improve clinical effect evaluation.

Abstract Background Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. Results We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. Conclusions For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.

ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single ABCE gene encoding the critical translational factor ABCE1. In several plant species, including Arabidopsis thaliana and Oryza sativa, two or more ABCE gene copies have been identified, however information related to plant ABCE gene family is still missing. In this study we retrieved ABCE gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to A. thaliana ABCE2 gene (AtABCE2). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of AtABCE2 and its paralogue AtABCE1 using genomic sequences of 1,135 A. thaliana ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight ABCE genes, suggesting that in plants ABCE genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that Brassicaceae and Poaceae families have independently undergone lineage-specific split of the ancestral ABCE gene. Other plant species have gained ABCE gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts ABCE gene family size. Deeper analysis of AtABCE2 and AtABCE1 from 1,135 A. thaliana ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in AtABCE2 compared to AtABCE1 is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor. [ABSTRACT FROM AUTHOR]

Background: Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. Results: We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. Conclusions: For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins. [ABSTRACT FROM AUTHOR]

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence–absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex. [ABSTRACT FROM AUTHOR]

The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses. [ABSTRACT FROM AUTHOR]

Lyme borreliosis (LB) is the most common vector‐borne disease in the Northern Hemisphere caused by spirochetes belonging to the Borrelia burgdorferi sensu lato (Bbsl) complex. Borrelia spirochetes circulate in obligatory transmission cycles between tick vectors and different vertebrate hosts. To successfully complete this complex transmission cycle, Bbsl encodes for an arsenal of proteins including the PFam54 protein family with known, or proposed, influences to reservoir host and/or vector adaptation. Even so, only fragmentary information is available regarding the naturally occurring level of variation in the PFam54 gene array especially in relation to Eurasian‐distributed species. Utilizing whole genome data from isolates (n = 141) originated from three major LB‐causing Borrelia species across Eurasia (B. afzelii, B. bavariensis, and B. garinii), we aimed to characterize the diversity of the PFam54 gene array in these isolates to facilitate understanding the evolution of PFam54 paralogs on an intra‐ and interspecies level. We found an extraordinarily high level of variation in the PFam54 gene array with 39 PFam54 paralogs belonging to 23 orthologous groups including five novel paralogs. Even so, the gene array appears to have remained fairly stable over the evolutionary history of the studied Borrelia species. Interestingly, genes outside Clade IV, which contains genes encoding for proteins associated with Borrelia pathogenesis, more frequently displayed signatures of diversifying selection between clades that differ in hypothesized vector or host species. This could suggest that non‐Clade IV paralogs play a more important role in host and/or vector adaptation than previously expected, which would require future lab‐based studies to validate. [ABSTRACT FROM AUTHOR]

Millions of years of isolation have given Madagascar a unique flora that still reflects some of its relationship with the continents of Africa and India. Here, the complete chloroplast sequence of Beilschmiedia moratii, a tropical tree in Madagascar, was determined. The plastome, with a length of 158,410 bp, was 143 bp and 187 bp smaller than those of two closely related species, B. pierreana and Potameia microphylla, in sub-Saharan Africa and Madagascar with published sequences, respectively. A total of 124 repeats and 114 simple sequence repeats (SSRs) were detected in the plastome of B. moratii. Six highly variable regions, including ndhF, ndhF-rpl32, trnC-petN, pebE-petL, rpl32-trnL, and ycf1, among the three African species were identified and 1151 mutation events, including 14 SVs, 351 indels, and 786 substitutions, were accurately located. There were 634 mutation events between B. moratii and P. microphylla with a mean nucleotide variability (π) value of 0.00279, while there were 827 mutation events between B. moratii and B. pierreana with a mean π value of 0.00385. The Ka/Ks ratios of 86 protein-coding genes in the three African species were less than 1, and the mean value between B. moratii and P. microphylla was 0.184, while the mean value between B. moratii and B. pierreana was 0.286. In this study, the plastid genomes of the three African Beilschmiediineae species were compared for the first time and revealed that B. moratii and P. microphylla from Madagascar were relatively conserved, with low mutation rates and slower evolutionary rates. [ABSTRACT FROM AUTHOR]

In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues. [ABSTRACT FROM AUTHOR]

Abstract Background Caffeic acid O-methyltransferase (COMT) is a key enzyme that regulates melatonin synthesis and is involved in regulating the growth, development, and response to abiotic stress in plants. Tea plant is a popular beverage consumed worldwide, has been used for centuries for its medicinal properties, including its ability to reduce inflammation, improve digestion, and boost immune function. By analyzing genetic variation within the COMT family, while helping tea plants resist adversity, it is also possible to gain a deeper understanding of how different tea varieties produce and metabolize catechins, then be used to develop new tea cultivars with desired flavor profiles and health benefits. Results In this study, a total of 25 CsCOMT genes were identified based on the high-quality tea (Camellia sinensis) plant genome database. Phylogenetic tree analysis of CsCOMTs with COMTs from other species showed that COMTs divided into four subfamilies (Class I, II, III, IV), and CsCOMTs was distributed in Class I, Class II, Class III. CsCOMTs not only undergoes large-scale gene recombination in pairs internally in tea plant, but also shares 2 and 7 collinear genes with Arabidopsis thaliana and poplar (Populus trichocarpa), respectively. The promoter region of CsCOMTs was found to be rich in cis-acting elements associated with plant growth and stress response. By analyzing the previously transcriptome data, it was found that some members of CsCOMT family exhibited significant tissue-specific expression and differential expression under different stress treatments. Subsequently, we selected six CsCOMTs to further validated their expression levels in different tissues organ using qRT-PCR. In addition, we silenced the CsCOMT19 through virus-induced gene silencing (VIGS) method and found that CsCOMT19 positively regulates the synthesis of melatonin in tea plant. Conclusion These results will contribute to the understanding the functions of CsCOMT gene family and provide valuable information for further research on the role of CsCOMT genes in regulating tea plant growth, development, and response to abiotic stress.

Sirtuins are a family of proteins that protect against cellular injury and aging; understanding their evolution should reveal fundamental mechanisms governing longevity. "Early-branching" animals such as sea sponges and jellyfish have been understudied in previous analyses of sirtuin diversity. These organisms not only hold important positions at the base of the evolutionary tree, but also have unique aging dynamics that defy convention, such as quasi-immortality and high regenerative capacity. In this study, we survey the evolution of sirtuin proteins in animals, with a focus on the oldest living lineages. We describe previously unrecognized expansions of "Class IV" and "Class I" sirtuins around the origin of animals, raising the number of sirtuin families in the last common ancestor to at least nine. Most of these undescribed sirtuins have been lost in vertebrates and other bilaterian animals. Our work also clarifies the evolution of PNC1 and NAMPT enzymes that carry out the rate-limiting step in sirtuin-related NAD+ biosynthesis. The genes for PNC1 and NAMPT enzymes were both present in the first animals, with the genes being lost a minimum of 11 and 13 times, respectively, over the course of animal evolution. We propose that species with these ancestral gene repertoires are ideal model organisms for studying the genetic regulation of animal longevity and will provide clues to increasing longevity in humans.

SUMMARY: Pungent capsaicinoid is synthesized only in chili pepper (Capsicum spp.). The production of vanillylamine from vanillin is a unique reaction in the capsaicinoid biosynthesis pathway. Although putative aminotransferase (pAMT) has been isolated as the vanillylamine synthase gene, it is unclear how Capsicum acquired pAMT. Here, we present a phylogenetic overview of pAMT and its homologs. The Capsicum genome contained 5 homologs, including pAMT, CaGABA‐T1, CaGABA‐T3, and two pseudogenes. Phylogenetic analysis indicated that pAMT is a member of the Solanaceae cytoplasmic GABA‐Ts. Comparative genome analysis found that multiple copies of GABA‐T exist in a specific Solanaceae genomic region, and the cytoplasmic GABA‐Ts other than pAMT are located in the region. The cytoplasmic GABA‐T was phylogenetically close to pseudo‐GABA‐T harboring a plastid transit peptide (pseudo‐GABA‐T3). This suggested that Solanaceae cytoplasmic GABA‐Ts occurred via duplication of a chloroplastic GABA‐T ancestor and subsequent loss of the plastid transit signal. The cytoplasmic GABA‐T may have been translocated from the specific Solanaceae genomic region during Capsicum divergence, resulting in the current pAMT locus. A recombinant protein assay demonstrated that pAMT had higher vanillylamine synthase activity than those of other plant GABA‐Ts. pAMT was expressed exclusively in the placental septum of mature green fruit, whereas tomato orthologs SlGABA‐T2/4 exhibit a ubiquitous expression pattern in plants. These findings suggested that both the increased catalytic efficiency and transcriptional changes in pAMT may have contributed to establish vanillylamine synthesis in the capsaicinoid biosynthesis pathway. This study provides insights into the establishment of pungency in the evolution of chili peppers. Significance Statement: Chili pepper vanillylamine synthase (pAMT) in capsaicin biosynthesis pathway belongs to the Solanaceae cytoplasmic GABA‐Ts, which originated via duplication of a chloroplastic ancestor and exhibits higher catalytic efficiency and placenta‐specific expression, compared with other close‐related GABA‐Ts. This study presents an intriguing case of how a primary metabolism enzyme evolved into a key enzyme that contributes to lineage‐specific secondary metabolite biosynthesis. [ABSTRACT FROM AUTHOR]

The aim of this work is the full characterization of all the nocturnin (noc) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of noc in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for noc-a (noc-aa and noc-ab) with two splice variants (I and II), and only one for noc-b (noc-bb) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three noc isoforms. A synteny analysis based on the localization of noc genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of noc in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the noc paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization. [ABSTRACT FROM AUTHOR]

ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single ABCE gene encoding the critical translational factor ABCE1. In several plant species, including Arabidopsis thaliana and Oryza sativa, two or more ABCE gene copies have been identified, however information related to plant ABCE gene family is still missing. In this study we retrieved ABCE gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to A. thaliana ABCE2 gene (AtABCE2). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of AtABCE2 and its paralogue AtABCE1 using genomic sequences of 1,135 A. thaliana ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight ABCE genes, suggesting that in plants ABCE genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that Brassicaceae and Poaceae families have independently undergone lineage-specific split of the ancestral ABCE gene. Other plant species have gained ABCE gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts ABCE gene family size. Deeper analysis of AtABCE2 and AtABCE1 from 1,135 A. thaliana ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in AtABCE2 compared to AtABCE1 is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.

Abstract Lyme borreliosis (LB) is the most common vector‐borne disease in the Northern Hemisphere caused by spirochetes belonging to the Borrelia burgdorferi sensu lato (Bbsl) complex. Borrelia spirochetes circulate in obligatory transmission cycles between tick vectors and different vertebrate hosts. To successfully complete this complex transmission cycle, Bbsl encodes for an arsenal of proteins including the PFam54 protein family with known, or proposed, influences to reservoir host and/or vector adaptation. Even so, only fragmentary information is available regarding the naturally occurring level of variation in the PFam54 gene array especially in relation to Eurasian‐distributed species. Utilizing whole genome data from isolates (n = 141) originated from three major LB‐causing Borrelia species across Eurasia (B. afzelii, B. bavariensis, and B. garinii), we aimed to characterize the diversity of the PFam54 gene array in these isolates to facilitate understanding the evolution of PFam54 paralogs on an intra‐ and interspecies level. We found an extraordinarily high level of variation in the PFam54 gene array with 39 PFam54 paralogs belonging to 23 orthologous groups including five novel paralogs. Even so, the gene array appears to have remained fairly stable over the evolutionary history of the studied Borrelia species. Interestingly, genes outside Clade IV, which contains genes encoding for proteins associated with Borrelia pathogenesis, more frequently displayed signatures of diversifying selection between clades that differ in hypothesized vector or host species. This could suggest that non‐Clade IV paralogs play a more important role in host and/or vector adaptation than previously expected, which would require future lab‐based studies to validate.

The impact of global warming is increasing and thus exacerbating environmental stresses that affect plant yield and distribution, including the Eriobotrya japonica Lindl (Loquat tree). Eriobotrya japonica, a member of the Rosaceae family, is valued not only for its nutritious fruit but also for its medicinal purposes, landscape uses, and other pharmacological benefits. Nonetheless, the productivity of Eriobotrya japonica has raised a lot of concern in the wake of adverse environmental conditions. Understanding the characteristics of the LRR-RLK gene family in loquat is crucial, as these genes play vital roles in plant stress responses. In this study, 283 LRR-RLK genes were identified in the genome of E. japonica that were randomly positioned on 17 chromosomes and 24 contigs. The 283 EjLRR-RLK proteins clustered into 21 classes and subclasses in the phylogenetic analysis based on domain and protein arrangements. Further explorations in the promoter regions of the EjLRR-RLK genes showed an abundance of cis-regulatory elements that functioned in growth and development, phytohormone, and biotic and abiotic responses. Most cis-elements were present in the biotic and abiotic responses suggesting that the EjLRR-RLK genes are invested in regulating both biotic and abiotic stresses. Additional investigations into the responses of EjLRR-RLK genes to abiotic stress using the RT-qPCR revealed that EjLRR-RLK genes respond to abiotic stress, especially heat and salt stresses. Particularly, EjapXI-1.6 and EjapI-2.5 exhibited constant upregulation in all stresses analyzed, indicating that these may take an active role in regulating abiotic stresses. Our findings suggest the pivotal functions of EjLRR-RLK genes although additional research is still required. This research aims to provide useful information relating to the characterization of EjLRR-RLK genes and their responses to environmental stresses, establishing a concrete base for the following research.

Abstract Background Oligodendroglioma is known for its relatively better prognosis and responsiveness to radiotherapy and chemotherapy. However, little is known about the evolution of genetic changes as oligodendroglioma progresses. Methods In this study, we evaluated gene evolution invivo during tumor progression based on deep whole‐genome sequencing data (ctDNA). We analyzed longitudinal genomic data from six patients during tumor evolution, of which five patients developed distant recurrence. Results Whole‐exome sequencing demonstrated that the rate of shared mutations between the primary and recurrent samples was relatively low. In two cases, even well‐known major driver mutations in CIC and FUBP1 that were detected in primary tumors were not detected in the relapse samples. Among these cases, two patients had a conversion from the IDH mutation in the originating state to the IDH1 wild state during the process of gene evolution under chemotherapy treatment, indicating that the cell phenotype and genetic characteristics of oligodendroglioma may change during tumor evolution. Two patients received long‐term temozolomide (TMZ) treatment before the operation, and we found that recurrence tumors harbored mutations in the PI3K/AKT and Sonic hedgehog (SHh) signaling pathways. Hypermutation occurred with mutations in MMR genes in one patient, contributing to the rapid progression of the tumor. Conclusion Oligodendroglioma displayed great spatial and temporal heterogeneity during tumor evolution. The PI3K/AKT and SHh signaling pathways may play an important role in promoting treatment resistance and distant relapse during oligodendroglioma evolution. In addition, there was a tendency to increase the degree of tumor malignancy during evolution. Distant recurrence may be a later event duringoligodendroglioma progression. ClinicalTrials.gov, Identifier: NCT05512325.

Summary: Maleae is one of the most widespread tribes of Rosaceae and includes several important fruit crops and ornamental plants.We used nuclear genes from 62 transcriptomes/genomes, including 26 newly generated transcriptomes, to reconstruct a well‐supported phylogeny and study the evolution of fruit and leaf morphology and the possible effect of whole genome duplication (WGD).Our phylogeny recovered 11 well‐supported clades and supported the monophyly of most genera (except Malus, Sorbus, and Pourthiaea) with at least two sampled species. A WGD was located to the most recent common ancestor (MRCA) of Maleae and dated to c. 54 million years ago (Ma) near the Early Eocene Climatic Optimum, supporting Gillenieae (x = 9) being a parental lineage of Maleae (x = 17) and including duplicate regulatory genes related to the origin of the fleshy pome fruit. Whole genome duplication‐derived paralogs that are retained in specific lineages but lost in others are predicted to function in development, metabolism, and other processes. An upshift of diversification and innovations of fruit and leaf morphologies occurred at the MRCA of the Malinae subtribe, coinciding with the Eocene–Oligocene transition (c. 34 Ma), following a lag from the time of the WGD event.Our results provide new insights into the Maleae phylogeny, its rapid diversification, and morphological and molecular evolution. [ABSTRACT FROM AUTHOR]

Family I84 serine protease inhibitors are believed to be mollusk specific proteins involved in host defense. The molecular evolution of the family, however, remains to be understood. In this study, the genes of Family I84 protease inhibitors in 3 bivalves, Crassostrea gigas, Crassostrea virginica and Tegillarca granosa, were analyzed at the genomic level. A total of 66 Family I84 genes (22 in C. gigas, 28 in C. virginica and 16 in T. granosa) were identified from the 3 species. They distributed unevenly in the genomes involving 4 chromosomes in C. gigas and 5 chromosomes in C. virginica and T. granosa and some genes were tandemly duplicated. Most genes had 3 exons with 12 genes having 4 exons and 1 gene having 2 exons. All genes but 1 from C. gigas and 1 from T. granosa encoded peptides with a signal sequence at the N-terminus, and the properties of the predicted mature molecules were similar. Four conserved motifs were identified in the 66 amino acid sequences. Collinear analysis revealed higher collinearity between the 2 oyster species in general genes and in Family I84 genes. Phylogenetic analysis of the 66 genes with those previously reported from 3 other bivalves and 1 gastropod showed that Family I84 protease inhibitor genes from the same species tended to be grouped together in terminal branches of the constructed Maximum likelihood tree, but most internal nodes were poorly supported by the bootstrap values. In addition, differences in expression patterns between the genes of a same species were observed in the developmental stages and tissues of C. gigas and T. granosa. Moreover, the co-expression of genes within Family I84 and Family I84 genes with non-Family I84 were also detected in C. gigas and T. granosa. These results suggested that Family I84 protease inhibitor genes evolved by active duplications and structural and functional diversifications after the speciation of related mollusks, and the diversified protease inhibitor family was likely multifunctional. [ABSTRACT FROM AUTHOR]

Only few glufosinate-tolerant genes, such as phosphinothricin acetyltransferase (PAT) and bialaphos resistance (bar) identified from Streptomyces, are currently available for developing genetically modified rice in agricultural application. Following the rapid development of genome editing technology, generation of novel glufosinate-tolerant gene resources through artificial evolution of endogenous genes is more promising and highly desirable in rice molecular breeding program. In this study, the endogenous Glutamine synthetase1 (OsGS1) was artificially evolved by base-editing-mediated gene evolution (BEMGE) in rice cells to create novel alleles conferring glufosinate tolerance in rice germplasms. Two novel glufosinate-tolerant OsGS1 alleles (OsGS1-AVPS and OsGS1-+AF) and one reported tolerant allele (OsGS1-SGTA) were successfully identified from approximately 4200 independent hygromycin-tolerant calli. Germination assays and spray tests revealed that these three OsGS1 alleles confer glufosinate tolerance in rice. Furthermore, OsGS1-AVPS and OsGS1-SGTA were quickly deployed into the elite rice cultivar Nangeng 46 through precise base editing. Overall, our results demonstrate the feasibility of developing glufosinate-tolerant rice by editing an endogenous rice gene in molecular breeding programs.

The editorial in Frontiers in Genetics discusses comparative and evolutionary analyses of organelle genomes, focusing on studies of chloroplast and mitochondrial genomes in non-model species. The paper highlights genomic rearrangements and gene evolution in parasitic plants like Love Vines and the impact of a parasitic lifestyle on chloroplast genomes. Additionally, the editorial covers the sequencing of the mitochondrial genome of the Asian freshwater fish Osteochilus salsburyi and the evolution of the CHS gene in plants. Lastly, it explores population genetics in rats, specifically the Brown Rat and Oriental Rat, to understand genetic diversity and migration patterns. The research topic provides insights into the potential of organelle genome analyses for scientific studies and highlights the importance of new sequencing technologies for future research. [Extracted from the article]

Plant architecture traits are a pivotal component in crop improvement and one of the key aspects of breeding programs for centuries. Among architecture traits, leaves and roots angle are most important whereas roots angle is considered to play a vital role in plant response to drought avoidance. Several genes regulating drought response reported in plants, such as LAZY1, Deeper Rooting 1 (DRO1), and Tiller angle control 1 (TAC1), belong to the IGT family. The wheat (Triticum aestivum L.) genome is complex because it consists of three subgenomes A, B, and D. A genome-wide (A, B, and D) identification and characterization of IGT family genes in wheat was reported in this study. A total of 12 IGT genes were identified and categorized based on phylogenetic reconstruction and gene structure analysis. These genes were distributed on chromosomes 2, 5, and 6 corresponding to the A, B, and D genomes of wheat. Most of the genes showed similar structures. Cis-regulatory elements in the promoter regions interpreted the presence of light, stress, development, and hormone-related elements. Five miRNAs (tae-miR9773, tae-miR531, tae-miR9678–3p, tae-miR9781, and tae-miR5049–3p) were predicted which target these TaIGT. Both the RNA-seq-based transcriptomic and real-time gene expression analysis suggested that all the genes are strongly expressed in roots, thus showing function conservation. 3D models and molecular docking of TaIGT were also carried out systematically, and binding patterns and the orientation of ligands in the active site of proteins were predicted. This study delves further into TaIGT genes and their expression patterns. The findings of this work are important for understanding the molecular control of root development and for future functional characterization of wheat root architecture genes. Key message: IGT gene family has not been identified and characterized and we identified 12 genes strongly expressing in roots. Furthermore, five miRNAs were predicted and could have a role in root conservation.

De novo genes are genes that emerge as new genes in some species, such as primate de novo genes that emerge in certain primate species. Over the past decade, a great deal of research has been conducted regarding their emergence, origins, functions, and various attributes in different species, some of which have involved estimating the ages of de novo genes. However, limited by the number of species available for whole-genome sequencing, relatively few studies have focused specifically on the emergence time of primate de novo genes. Among those, even fewer investigate the association between primate gene emergence with environmental factors, such as paleoclimate (ancient climate) conditions. This study investigates the relationship between paleoclimate and human gene emergence at primate species divergence. Based on 32 available primate genome sequences, this study has revealed possible associations between temperature changes and the emergence of de novo primate genes. Overall, findings in this study are that de novo genes tended to emerge in the recent 13 MY when the temperature continues cooling, which is consistent with past findings. Furthermore, in the context of an overall trend of cooling temperature, new primate genes were more likely to emerge during local warming periods, where the warm temperature more closely resembled the environmental condition that preceded the cooling trend. Results also indicate that both primate de novo genes and human cancer-associated genes have later origins in comparison to random human genes. Future studies can be in-depth on understanding human de novo gene emergence from an environmental perspective as well as understanding species divergence from a gene emergence perspective. [ABSTRACT FROM AUTHOR]

Background: Oligodendroglioma is known for its relatively better prognosis and responsiveness to radiotherapy and chemotherapy. However, little is known about the evolution of genetic changes as oligodendroglioma progresses. Methods: In this study, we evaluated gene evolution invivo during tumor progression based on deep whole‐genome sequencing data (ctDNA). We analyzed longitudinal genomic data from six patients during tumor evolution, of which five patients developed distant recurrence. Results: Whole‐exome sequencing demonstrated that the rate of shared mutations between the primary and recurrent samples was relatively low. In two cases, even well‐known major driver mutations in CIC and FUBP1 that were detected in primary tumors were not detected in the relapse samples. Among these cases, two patients had a conversion from the IDH mutation in the originating state to the IDH1 wild state during the process of gene evolution under chemotherapy treatment, indicating that the cell phenotype and genetic characteristics of oligodendroglioma may change during tumor evolution. Two patients received long‐term temozolomide (TMZ) treatment before the operation, and we found that recurrence tumors harbored mutations in the PI3K/AKT and Sonic hedgehog (SHh) signaling pathways. Hypermutation occurred with mutations in MMR genes in one patient, contributing to the rapid progression of the tumor. Conclusion: Oligodendroglioma displayed great spatial and temporal heterogeneity during tumor evolution. The PI3K/AKT and SHh signaling pathways may play an important role in promoting treatment resistance and distant relapse during oligodendroglioma evolution. In addition, there was a tendency to increase the degree of tumor malignancy during evolution. Distant recurrence may be a later event duringoligodendroglioma progression. ClinicalTrials.gov, Identifier: NCT05512325. [ABSTRACT FROM AUTHOR]

MADS-box is an important transcriptional regulatory element in plant growth. The MIKC-type MADS-box genes play important roles. However, the identification and evolutionary investigation of MIKC-type MADS-box family members in Rosaceae have been inadequate. Therefore, based on whole-genome data from Prunus dulcis, Prunus salicina, Prunus armeniaca, Prunus persica, Prunus mira, and Amygdalus nana, we depicted the evolution and divergence patterns of MIKC-type MADS-box family genes. In this study, we found 222 MIKC-type MADS-box genes from six Rosaceae species. These genes were classified into five clades, and only motif 1 was identified across all MIKC-type MADS-box proteins, except PdMADS42 and PmiMADS16. The structural properties of these genes significantly varied in sequence lengths between species, despite the high levels of similarity in exon lengths and numbers. MIKC-type MADS-box genes were found to have mostly been limited through purifying selection processes. Remarkably divergent regions were found inside the MIKC-type MADS-box genes' domains, where clade III displayed more conserved activities and may have retained more original functions over the evolutionary process; clade I, on the other hand, may have undergone substantial functional limitations in a specific functional role. These findings provide the groundwork for future research into the molecular evolutionary processes of the plant MIKC-type MADS-box gene family. [ABSTRACT FROM AUTHOR]

Sperm motility‐initiating substance (SMIS) is an oviductal protein critical for internal fertilization in urodeles. It contributes to the establishment of various reproductive modes in amphibians and is thus a unique research model for the gene evolution of gamete‐recognizing ligands that have diversified among animal species. In this study, a paralogous SMIS gene, smis2, was identified via the RNA sequencing of the oviduct of the newt, Cynops pyrrhogaster. The base sequence of the smis2 gene was homologous (˃90%) to that of the original smis gene (smis1), and deduced amino acid sequences of both genes conserved six cysteine residues essential for the cysteine knot motif. Furthermore, smis2 complementary DNA was identified in the oviduct of Cynops ensicauda, and the base substitution patterns also suggested that the smis gene was duplicated in the Salamandridae. Nonsynonymous/synonymous substitution ratios of smis1 and smis2 genes were 0.79 and 2.6, respectively, suggesting that smis2 gene evolution was independently driven by positive selection. Amino acid substitutions were concentrated in the cysteine knot motif of SMIS2. The smis2 gene was expressed in some organs in addition to the oviduct; in contrast, SMIS1 was only expressed in the oviduct. The SMIS2 protein was suggested to be produced and secreted at least in the oviduct and redundantly act in sperm. These results suggest that smis1 plays the original role in the oviduct, whereas smis2 may undergo neofunctionalization, which rarely occurs in gene evolution. [ABSTRACT FROM AUTHOR]

Abstract The vertebrate sodium–iodide symporter (NIS or SLC5A5) transports iodide into the thyroid follicular cells that synthesize thyroid hormone. The SLC5A protein family includes transporters of vitamins, minerals, and nutrients. Disruption of SLC5A5 function by perchlorate, a pervasive environmental contaminant, leads to human pathologies, especially hypothyroidism. Perchlorate also disrupts the sexual development of model animals, including threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), but the mechanism of action is unknown. To test the hypothesis that SLC5A5 paralogs are expressed in tissues necessary for the development of reproductive organs, and therefore are plausible candidates to mediate the effects of perchlorate on sexual development, we first investigated the evolutionary history of Slc5a paralogs to better understand potential functional trajectories of the gene family. We identified two clades of slc5a paralogs with respect to an outgroup of sodium/choline cotransporters (slc5a7); these clades are the NIS clade of sodium/iodide and lactate cotransporters (slc5a5, slc5a6, slc5a8, slc5a8, and slc5a12) and the SGLT clade of sodium/glucose cotransporters (slc5a1, slc5a2, slc5a3, slc5a4, slc5a10, and slc5a11). We also characterized expression patterns of slc5a genes during development. Stickleback embryos and early larvae expressed NIS clade genes in connective tissue, cartilage, teeth, and thyroid. Stickleback males and females expressed slc5a5 and its paralogs in gonads. Single‐cell transcriptomics (scRNA‐seq) on zebrafish sex‐genotyped gonads revealed that NIS clade‐expressing cells included germ cells (slc5a5, slc5a6a, and slc5a6b) and gonadal soma cells (slc5a8l). These results are consistent with the hypothesis that perchlorate exerts its effects on sexual development by interacting with slc5a5 or its paralogs in reproductive tissues. These findings show novel expression domains of slc5 genes in stickleback and zebrafish, which suggest similar functions across vertebrates including humans, and provide candidates to mediate the effects of perchlorate on sexual development.

Litsea, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of Litsea taxa. One is composed of 16 Litsea taxa and two Lindera taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.

Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and may act as potential genetic determinants of lineage-specific, biological properties. Here, we explore the TRGs of highly diverse and economically important Bacillus bacteria by examining commonly used TRG identification parameters and data sources. We show the significant effects of sequence similarity thresholds, composition, and the size of the reference database in the identification process. Subsequently, we applied stringent TRG search parameters and expanded the identification procedure by incorporating an analysis of noncoding and non-syntenic regions of non- Bacillus genomes. A multiplex annotation procedure minimized the number of false-positive TRG predictions and showed nearly one-third of the alleged TRGs could be mapped to genes missed in genome annotations. We traced the putative origin of TRGs by identifying homologous, noncoding genomic regions in non- Bacillus species and detected sequence changes that could transform these regions into protein-coding genes. In addition, our analysis indicated that Bacillus TRGs represent a specific group of genes mostly showing intermediate sequence properties between genes that are conserved across multiple taxa and nonannotated peptides encoded by open reading frames. [ABSTRACT FROM AUTHOR]

Warm temperature acclimation-related 65-kDa proteins (Wap65s) are fish plasma acute-phase glycoproteins homologous to hemopexin with high affinity and clearance for heme. The study characterized Mswap65-1 and Mswap65-2 genes in Micropterus salmoides. Structural analysis showed Ms Wap65s contained conserved heme-binding sites. Ms Wap65-1 had a chloride-binding site similar to hemopexin, while Ms Wap65-2 had an additional calcium-binding site. Phylogenetic and Ka / Ks analysis showed that fish Wap65s were evolutionarily conserved and underwent strong purifying selection. Functional divergence analysis indicated that fish Wap65-2 retained the putative function of ancestral Wap65, while Wap65-1 underwent neofunctional differentiation. QPCR showed Mswap65 s were predominantly expressed in liver, but prolonged hyperthermy inhibited Mswap65-2 expression. Mswap65-2 expression was up-regulated in liver and spleen after Nocardia seriolae infection, while Mswap65-1 was down-regulated. Ms Wap65-2 may be associated with pathogenesis and play potential role in pathogen resistance. LMBV infection resulted in both significant downregulation of Mswap65s were both significantly down-regulated, with differences observed between sexes. We speculated the immune system might suppress expression after viral infection. Exogenous r Ms Wap65s were prepared, and injection of r Ms Wap65s alleviated phenylhydrazine-induced hemolysis and inhibited increases in heme, complement C3 and inflammatory symptoms. Our results contribute to an advanced understanding of the functions and mechanisms of Ms Wap65s in stress resistance. [ABSTRACT FROM AUTHOR]

The AqE gene encodes a sulfolactate dehydrogenase-like enzyme of the LDH2/MDG2 oxidoreductase family. The gene is found in bacteria and fungi, as well as in animals and plants whose lifestyles are associated with aquatic environments. The AqE gene is present in arthropods and, in particular, insects that are predominantly terrestrial. The distribution and structure of AqE was studied in insects in order to trace its evolutionary fate. The AqE gene was found to be absent from certain insect orders and suborders, being apparently lost. AqE duplication or multiplication was observed in some orders. AqE was found to vary both in length and intron–exon structure, from intronless to multi-intron. An ancient nature was demonstrated for AqE multiplication in insects, while younger duplications were also detected. It was assumed that a new function might be acquired by the gene with the formation of paralogs. [ABSTRACT FROM AUTHOR]

Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs. [ABSTRACT FROM AUTHOR]

WRKY transcription factors (TFs), one of the largest TF families, serve critical roles in the regulation of secondary metabolite production. However, little is known about the expression pattern of WRKY genes during the germination and maturation processes of Toona sinensis buds. In the present study, the new assembly of the T. sinensis genome was used for the identification of 78 TsWRKY genes, including gene structures, phylogenetic features, chromosomal locations, conserved protein domains, cis-regulatory elements, synteny, and expression profiles. Gene duplication analysis revealed that gene tandem and segmental duplication events drove the expansion of the TsWRKYs family, with the latter playing a key role in the creation of new TsWRKY genes. The synteny and evolutionary constraint analyses of the WRKY proteins among T. sinensis and several distinct species provided more detailed evidence of gene evolution for TsWRKYs. Besides, the expression patterns and co-expression network analysis show TsWRKYs may multi-genes co-participate in regulating terpenoid biosynthesis. The findings revealed that TsWRKYs potentially play a regulatory role in secondary metabolite synthesis, forming the basis for further functional characterization of WRKY genes with the intention of improving T. sinensis. [ABSTRACT FROM AUTHOR]

ObjectiveTo analyze the characteristics of whole genome sequences of H3N2 influenza virus strains isolated in Guangzhou city for providing reference data to the prevention and control of H3N2 influenza.MethodsWhole-genome sequencing was performed for 13 strains of H3N2 influenza virus isolated in Guangzhou city in 2019 and the sequencing results were analyzed with bioinformatics software. Gene segments of H3N2 influenza vaccine strains recommended by World Health Organization for the northern hemisphere population over the years were extracted from the Global Initiative on Sharing Avian Influenza Data (GISAID) as the reference sequences.ResultsFor the 13 virus strains sequenced, the lowest nucleotide homology was 94% and the highest was 100%. Compared to the reference sequences, the gene with the greatest difference was NA (94% – 100%) and that with the least difference was PA (98.9% – 100%). The nucleotide variation rate of was the highest for NA gene (8.37%) and the lowest for PA gene (2.14%). All genes of the isolated strains, including both from out-patients under surveillance and from outbreak cases, belong to those of the same evolutionary branch of the vaccine strain (A/Hong Kong/2671/2019 H3N2). The HA, PB2, PB1, NP, M and NS genes of the strains could be further divided into three small branches (group 1 – 3) based on their epidemic time. Group 1, 2, and 3 were prevalent during periods of January – August, November – December, and January – August/November – December of 2019, respectively.ConclusionThe H3N2 influenza virus strains isolated in Guangzhou in 2019 were on the same evolutionary branch to the vaccine strain. The isolated strains had the same evolutionary origin but there were diversities in evolutionary characteristics, homologies and the variation rates of the whole genome among the strains.

Mutants lacking wild-type MLO (Mildew resistance Locus O) proteins show broad-spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants, we analysed systematically genome-wide data from Fragaria vesca, Prunus persica, Prunus mume, Malus domestica, Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods. Using three phylogenetic methods (the neighbour-joining, maximum likelihood, and Bayesian methods), we identified 117 MLO genes from 6 Rosaceae species. The results of all three phylogenetic analysis methods supported that these genes were divided into six clades. Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues. The findings indicated that motif 2 might be shared by the MLO gene family. The structural features of these genes showed large variations in sequence length among different species, although the lengths and the numbers of exons exhibited high degrees of similarity. Selective pressure analysis showed extremely significant differences in all 6 clades, with 2, 1, and 1 site(s) under significant positive selection detected in clades III, IV, and VI, respectively. These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes. Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes. Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process. However, clade I may have undergone extensive altered functional constraints as a specialised functional role. Moreover, the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew, which then gradually evolved into functions such as the regulation of flower development, the control of root morphology, and seed evolution due to the different evolutionary rates after gene duplication. These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

Increasing numbers of small proteins with diverse physiological roles are being identified and characterized in both prokaryotic and eukaryotic systems, but the origins and evolution of these proteins remain unclear. Recent genomic sequence analyses in several organisms suggest that new functions encoded by small open reading frames (sORFs) may emerge de novo from noncoding sequences. However, experimental data demonstrating if and how randomly generated sORFs can confer beneficial effects to cells are limited. Here, we show that by upregulating hisB expression, de novo small proteins (≤50 amino acids in length) selected from random sequence libraries can rescue Escherichia coli cells that lack the conditionally essential SerB enzyme. The recovered small proteins are hydrophobic and confer their rescue effect by binding to the 5′ end regulatory region of the his operon mRNA, suggesting that protein binding promotes structural rearrangements of the RNA that allow increased hisB expression. This study adds RNA regulatory elements as another interacting partner for de novo proteins isolated from random sequence libraries and provides further experimental evidence that small proteins with selective benefits can originate from the expression of nonfunctional sequences.

DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Astrovirus is an emerging zoonotic pathogen. Rabbit astrovirus can cause diarrhea in rabbits, which brings great economic losses to the rabbit industry. In this study, a rabbit astrovirus strain named Z317 was successfully isolated from the carcasses of rabbits that suffered from diarrhea, and its whole genome sequence was obtained. In this study, we provide valuable data to help understand the variation and recombination of the virus, and lay a foundation for the prevention and control of the disease and molecular epidemiological research. Rabbit astrovirus (RAstV) is a pathogen that causes diarrhea in rabbits, with high infection rate at various stages, which can often cause secondary or mixed infections with other pathogens, bringing great economic losses to the rabbit industry. In this study, 10 samples were collected from cases of rabbits with diarrhea on a rabbit meat farm in the Shandong area of China. The positive sample for astrovirus detected by RT-PCR was inoculated into an RK 13 cell line. A rabbit astrovirus strain named Z317 was successfully isolated, which produced an obvious cytopathic effect 48 h post-inoculation in the RK 13 cell line. The genome structure of this isolate was studied by high-throughput sequencing, showing that the Z317 strain had the highest similarity with the American strain TN/2208/2010, with 92.43% nucleotide homology, belonging to group MRAstV-23. The basic properties of the Z317 capsid (Cap) protein were analyzed, and 10 liner B cell epitopes were screened with the online biosoft Bepipred 2.0 and SVMTriP, including 445–464, 186–205, 655–674, 88–107, 792–811, 45–64, and 257–276 amino acids. This is the first contribution concerning RAstV genomes in China; more studies are needed to understand the diversity and impact of RAstV on rabbit health. [ABSTRACT FROM AUTHOR]

The Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to cancer progression. In addition to well-known hotspot mutations in RNAase III domains, DICER1 is characterized by a wide spectrum of variants in all the functional domains; most are of uncertain significance and unstated clinical effects. Moreover, various new somatic DICER1 mutations continuously appear in cancer genome sequencing. The latest contemporary methods of variant effect prediction utilize machine learning algorithms on bulk data, yielding suboptimal correlation with biological data. Consequently, such analysis should be conducted based on the functional and structural characteristics of each protein, using a well-grounded targeted dataset rather than relying on large amounts of unsupervised data. Domains are the functional and evolutionary units of a protein; the analysis of the whole protein should be based on separate and independent examinations of each domain by their evolutionary reconstruction. Dicer represents a hallmark example of a multidomain protein, and we confirmed the phylogenetic multidomain approach being beneficial for the clinical effect prediction of Dicer variants. Because Dicer was suggested to have a putative role in hematological malignancies, we examined variants of DICER1 occurring outside the well-known hotspots of the RNase III domain in this type of cancer using phylogenetic reconstruction of individual domain history. Examined substitutions might disrupt the Dicer function, which was demonstrated by molecular dynamic simulation, where distinct structural alterations were observed for each mutation. Our approach can be utilized to study other multidomain proteins and to improve clinical effect evaluation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Bug, Moiseev, Porozov and Petukhova.)