Orthologous Pairs Research Articles

Increasing nitrogen use efficiency in agronomically important plants: An insight into gene characteristics on a genome-wide scale in barley

Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare).Using bioinformatics and functional genomics tools, we identified and characterized sixteen barley nitrogen metabolism-related gene families (HvNMGs) on a genome-wide scale, analysing gene features and evolution. These genes, located on six of seven barley chromosomes, are highly conserved in plants (including barley, rice, and Arabidopsis), as shown by phylogenetic analysis. We further explored the evolutionary relationships of NMGs through a genome-to-genome synteny analysis, which indicated higher conservation of NMGs between barley and other monocots, suggesting that these orthologous pairs predate species divergence. Protein-protein interaction analyses revealed that all of the HvNMGs show interactions, mainly with each other. The H. vulgare miRNAs target sites (hvu-miR) prediction identified six hvu-miR in 4 HvNMGs (HvGABA-T2, HvALDH10-1, HvALDH10-2 and HvARGAH), indicating their potential involvement in stress responses. The expression patterns analysis of publicly available RNA-seq data revealed that HvNMGs are expressed in all developmental stages of barley, and they respond to different stress conditions, indicating their essential role in plant growth, development and stress response. The organ-specific expression analysis, conducted using qPCR, of HvNMGs revealed higher expression of HvNiR and HvNRs in the leaf and significantly higher expression of HvARGAH and HvALDH10 in the spike than in other tissues, showing that some of the genes may be particularly important in some tissues than others. This data provides a foundation for understanding HvNMG function and could be used to improve barley yield by enhancing NUE — an important goal for both crop productivity and environmental sustainability.

Day-night gene expression reveals circadian gene disco as a candidate for diel-niche evolution in moths.

Temporal ecological niche partitioning is an underappreciated driver of speciation. While insects have long been models for circadian biology, the genes and circuits that allow adaptive changes in diel-niches remain poorly understood. We compared gene expression in closely related day- and night-active non-model wild silk moths, with otherwise similar ecologies. Using an ortholog-based pipeline to compare RNA-Seq patterns across two moth species, we find over 25 pairs of gene orthologs showing differential expression. Notably, the gene disco, involved in circadian control, optic lobe and clock neuron development in Drosophila, shows robust adult circadian mRNA cycling in moth heads. Disco is highly conserved in moths and has additional zinc-finger domains with specific nocturnal and diurnal mutations. We propose disco as a candidate gene for the diversification of temporal diel-niche in moths.

Genome-wide characterization of cytochrome P450 genes reveals the potential roles in fruit ripening and response to cold stress in tomato.

Plant cytochrome P450 (CYP) superfamily, the largest enzyme metabolism family, has been identified in many species and plays a vital role in plant development and stress response via secondary metabolite biosynthesis. A comprehensive identification and functional investigation of CYPs in tomato plants would contribute to deeper understanding of their biological significance. In this study, 268 tomato CYP genes were identified and found to be unevenly located on 12 chromosomes. Based on the phylogenetic analysis, these 268 SlCYPs were classed into two distinct clades (A-type and non-A-type) and nine clans, including 48 families. Moreover, 67 tandem and 22 WGD (whole genome duplication)/segmental duplication events were detected, of which 12 SlCYP genes experienced both WGD/segmental and tandem duplication events, indicating that tandem duplication plays a major role in the expansion of the SlCYP family. Besides, 48 pairs containing 41 SlCYP and 44 AtCYP genes were orthologous, while 216 orthologous pairs were obtained between tomato and potato. The expression level of all SlCYP genes in tomato tissues at different development stages was analyzed, and most expressed SlCYPs showed a tissue-specific pattern. Meanwhile, 143 differentially expressed SlCYPs were identified under cold stress. Furthermore, the RT-qPCR results indicated that SlCYPs may be involved in fruit ripening and cold tolerance in tomato seedlings. These findings provide valuable insights into the evolutionary relationships and functional characteristics of SlCYPs, which can be utilized for further investigation of fruit metabolic pathways and cold tolerance in tomato.

Comparative identification of WRKY transcription factors and transcriptional response to Ralstonia solanacearum in tomato

In order to study the responses of tomato (Solanum lycopersicum) WRKY TFs to bacterial wilt caused by Ralstonia solanacearum, the most up-to-date genomes and transcriptional profiles were used to identify WRKY TFs in control and infected inbred lines. In total, 85 tomato WRKY TFs were identified and categorized into groups I, IIa + b, IIc, IId + e, and III. These WRKYs, especially those from group IIe, were mainly distributed at chromosome ends and in clusters. More than 45 % and 70 % of tomato WRKYs exhibited intraspecific and interspecific synteny, respectively. Nearly 60 % of tomato WRKYs (mainly in groups I and IIc) formed 73 pairs of orthologs with WRKYs in Arabidopsis and pepper, with Ka/Ks less than 1. Sixteen tomato WRKYs (mainly in groups IIa + b and IIc) responded strongly to biotic stress, and 12 differentially expressed WRKYs (mainly in groups III and IIb) were identified. RT-qPCR revealed that tomato WRKYs could respond to bacterial wilt through positive (predominant) or negative regulation. In particular, the interaction between Solyc03g095770.3 (group III) and Solyc09g014990.4 (group I) may play an important role. In brief, WRKY TFs were comprehensively identified in tomato and several bacterial wilt responsive genes were screened.

Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt

BackgroundMost disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung tree.ResultsHere, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V. fordii and 149 in V. montana. Five VmNBS-LRR paralogous were predicted in V. montana, and 43 orthologous were detected between V. fordii and V. montana. The orthologous gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns in V. fordii and V. montana: Vf11G0978 showed downregulated expression in V. fordii, while its orthologous gene Vm019719 demonstrated upregulated expression in V. montana, indicating that this pair may be responsible for the resistance to Fusarium wilt in V. montana. Vm019719 from V. montana, activated by VmWRKY64, was shown to confer resistance to Fusarium wilt in V. montana by a virus-induced gene silencing (VIGS) experiment. However, in the susceptible V. fordii, its allelic counterpart, Vf11G0978, exhibited an ineffective defense response, attributed to a deletion in the promoter’s W-box element.ConclusionsThis study provides the first systematic analysis of NBS-LRR genes in the tung tree and identifies a candidate gene that can be utilized for marker-assisted breeding to control Fusarium wilt in V. fordii.

Comprehensive genomic exploration of class III peroxidase genes in guava unravels physiology, evolution, and postharvest storage responses

Peroxidases (PRXs) play multifaceted roles in plant growth, development, and stress responses. Here, we present a comprehensive analysis of the PRX gene family in guava, a globally significant fruit. In the guava genome, we identified 37 PRX genes, a number lower than that of Arabidopsis, suggesting a distinctive gene family expansion pattern. Phylogenetic analysis unveiled close relationships with Arabidopsis PRXs, with 12 PgPRX genes forming ortholog pairs, indicating a specific expansion pattern. Predictions placed most PRX proteins in the chloroplast and extracellular regions. Structural analysis of PgPRX proteins revealed commonalities in domain structures and motif organization. Synteny analysis underscored the dynamic role of segmental duplication in the evolution of guava's PRX genes. We explored the dynamic expression of PgPRX genes across guava tissues, exposing functional diversity. Furthermore, we examined changes in peroxidase levels and gene expressions during postharvest fruit storage, providing insights for preserving fruit quality. This study offers an initial genome-wide identification and characterization of Class III peroxidases in guava, laying the foundation for future functional analyses.

Genome-wide analysis of respiratory burst oxidase homolog gene family in pea (Pisum sativum L.).

Plant respiratory burst oxidase homologs (RBOHs) are key enzymes regulating superoxide production, which is important for plant development and responses to biotic and abiotic stresses. This study aimed to characterize the RBOH gene family in pea (Pisum sativum L.). Seven PsRBOH genes were identified in the pea genome and were phylogenetically clustered into five groups. Collinearity analyses of the RBOHs identified four pairs of orthologs between pea and soybean. The gene structure analysis showed that the number of exons ranged from 6 to 16. Amino acid sequence alignment, conserved domain, and conserved motif analyses showed that all seven PsRBOHs had typical features of plant RBOHs. The expression patterns of PsRBOH genes in different tissues provided suggested their roles in plant growth and organ development. In addition, the expression levels of PsRBOH genes under different abiotic stresses were analyzed via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The results demonstrated that PsRBOH genes exhibited unique stress-response characteristics, which allowed for functional diversity in response to different abiotic stresses. Furthermore, four PsRBOHs had a high probability of localization in the plasma membrane, and PsRBOH6 was localized to the plasma membrane and endoplasmic reticulum. The results of this study provide valuable information for further functional analysis of pea RBOH genes and their role in plant adaptation to climate-driven environmental constraints.

ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize.

Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.

Revisiting structural organization of proteins at high temperature from a network perspective

Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.

Identification of cell-type specific alternative transcripts in the multicellular alga Volvox carteri

BackgroundCell type specialization is a hallmark of complex multicellular organisms and is usually established through implementation of cell-type-specific gene expression programs. The multicellular green alga Volvox carteri has just two cell types, germ and soma, that have previously been shown to have very different transcriptome compositions which match their specialized roles. Here we interrogated another potential mechanism for differentiation in V. carteri, cell type specific alternative transcript isoforms (CTSAI).MethodsWe used pre-existing predictions of alternative transcripts and de novo transcript assembly with HISAT2 and Ballgown software to compile a list of loci with two or more transcript isoforms, identified a small subset that were candidates for CTSAI, and manually curated this subset of genes to remove false positives. We experimentally verified three candidates using semi-quantitative RT-PCR to assess relative isoform abundance in each cell type.ResultsOf the 1978 loci with two or more predicted transcript isoforms 67 of these also showed cell type isoform expression biases. After curation 15 strong candidates for CTSAI were identified, three of which were experimentally verified, and their predicted gene product functions were evaluated in light of potential cell type specific roles. A comparison of genes with predicted alternative splicing from Chlamydomonas reinhardtii, a unicellular relative of V. carteri, identified little overlap between ortholog pairs with alternative splicing in both species. Finally, we interrogated cell type expression patterns of 126 V. carteri predicted RNA binding protein (RBP) encoding genes and found 40 that showed either somatic or germ cell expression bias. These RBPs are potential mediators of CTSAI in V. carteri and suggest possible pre-adaptation for cell type specific RNA processing and a potential path for generating CTSAI in the early ancestors of metazoans and plants.ConclusionsWe predicted numerous instances of alternative transcript isoforms in Volvox, only a small subset of which showed cell type specific isoform expression bias. However, the validated examples of CTSAI supported existing hypotheses about cell type specialization in V. carteri, and also suggested new hypotheses about mechanisms of functional specialization for their gene products. Our data imply that CTSAI operates as a minor but important component of V. carteri cellular differentiation and could be used as a model for how alternative isoforms emerge and co-evolve with cell type specialization.

IFF: Identifying key residues in intrinsically disordered regions of proteins using machine learning.

Conserved residues in protein homolog sequence alignments are structurally or functionally important. For intrinsically disordered proteins or proteins with intrinsically disordered regions (IDRs), however, alignment often fails because they lack a steric structure to constrain evolution. Although sequences vary, the physicochemical features of IDRs may be preserved in maintaining function. Therefore, a method to retrieve common IDR features may help identify functionally important residues. We applied unsupervised contrastive learning to train a model with self-attention neuronal networks on human IDR orthologs. Parameters in the model were trained to match sequences in ortholog pairs but not in other IDRs. The trained model successfully identifies previously reported critical residues from experimental studies, especially those with an overall pattern (e.g., multiple aromatic residues or charged blocks) rather than short motifs. This predictive model can be used to identify potentially important residues in other proteins, improving our understanding of their functions. The trained model can be run directly from the Jupyter Notebook in the GitHub repository using Binder (mybinder.org). The only required input is the primary sequence. The training scripts are available on GitHub (https://github.com/allmwh/IFF). The training datasets have been deposited in an Open Science Framework repository (https://osf.io/jk29b).

The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles

The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, classification, conserved motifs, cis-elements, chromosomal locations, evolution and expression patterns of the PtGLK genes in the woody model plant Populus trichocarpa were analyzed in detail. In total, 55 putative PtGLKs (PtGLK1-PtGLK55) were identified and divided into 11 distinct subfamilies according to the gene structure, motif composition and phylogenetic analysis. Synteny analysis showed that 22 orthologous pairs and highly conservation between regions of GLK genes across P. trichocarpa and Arabidopsis were identified. Furthermore, analysis of the duplication events and divergence times provided insight into the evolutionary patterns of GLK genes. The previously published transcriptome data indicated that PtGLK genes exhibited distinct expression patterns in various tissues and different stages. Additionally, several PtGLKs were significantly upregulated under the responses of cold stress, osmotic stress, and methyl jasmonate (MeJA) and gibberellic acid (GA) treatments, implying that they might take part in abiotic stress and phytohormone responses. Overall, our results provide comprehensive information on the PtGLK gene family and elucidate the potential functional characterization of PtGLK genes in P. trichocarpa.

Predicting gene expression divergence between single-copy orthologs in two species.

Predicting gene expression divergence is integral to understanding the emergence of new biological functions and associated traits. Whereas several sophisticated methods have been developed for this task, their applications are either limited to duplicate genes or require expression data from more than two species. Thus, here we present PiXi, the first machine learning framework for predicting gene expression divergence between single-copy orthologs in two species. PiXi models gene expression evolution as an Ornstein-Uhlenbeck process, and overlays this model with multi-layer neural network, random forest, and support vector machine architectures for making predictions. It outputs the predicted class "conserved" or "diverged" for each pair of orthologs, as well as their predicted expression optima in the two species. We show that PiXi has high power and accuracy in predicting gene expression divergence between single-copy orthologs, as well as high accuracy and precision in estimating their expression optima in the two species, across a wide range of evolutionary scenarios, with the globally best performance achieved by a multi-layer neural network. Moreover, application of our best performing PiXi predictor to empirical gene expression data from single-copy orthologs residing at different loci in two species of Drosophila reveals that approximately 23% underwent expression divergence after positional relocation. Further analysis shows that several of these "diverged" genes are involved in the electron transport chain of the mitochondrial membrane, suggesting that new chromatin environments may impact energy production in Drosophila. Thus, by providing a toolkit for predicting gene expression divergence between single-copy orthologs in two species, PiXi can shed light on the origins of novel phenotypes across diverse biological processes and study systems.

Genome-Wide Analysis of the Wall-Associated Kinase (WAK) Genes in Medicago truncatula and Functional Characterization of MtWAK24 in Response to Pathogen Infection.

The wall-associated kinases (WAKs) can perceive and transmit extracellular signals as one kind of unique receptor-like kinases (RLKs) involved in the regulation of cell expansion, pathogen resistance and abiotic stress tolerance. To understand their potential roles and screen some key candidates in Medicago truncatula (M. truncatula), genome-wide identification and characterization of MtWAKs were conducted in this study. A total of 54 MtWAK genes were identified and classified into four groups based on their protein domains. They were distributed on all chromosomes, while most of them were clustered on chromosome 1 and 3. The synteny analysis showed that 11 orthologous pairs were identified between M. truncatula and Arabidopsis thaliana (A. thaliana) and 31 pairs between M. truncatula and Glycine max (G. max). The phylogenetic analysis showed that WAK-RLKs were classified into five clades, and they exhibited a species-specific expansion. Most MtWAK-RLKs had similar exon-intron organization and motif distribution. Multiple cis-acting elements responsive to phytohormones, stresses, growth and development were observed in the promoter regions of MtWAK-RLKs. In addition, the expression patterns of MtWAK-RLKs varied with different plant tissues, developmental stages and biotic and abiotic stresses. Interestingly, plasm membrane localized MtWAK24 significantly inhibited Phytophthora infection in tobacco. The study provides valuable information for characterizing the molecular functions of MtWAKs in regulation of plant growth, development and stress tolerance in legume plants.

FAS: assessing the similarity between proteins using multi-layered feature architectures.

Protein sequence comparison is a fundamental element in the bioinformatics toolkit. When sequences are annotated with features such as functional domains, transmembrane domains, low complexity regions or secondary structure elements, the resulting feature architectures allow better informed comparisons. However, many existing schemes for scoring architecture similarities cannot cope with features arising from multiple annotation sources. Those that do fall short in the resolution of overlapping and redundant feature annotations. Here, we introduce FAS, a scoring method that integrates features from multiple annotation sources in a directed acyclic architecture graph. Redundancies are resolved as part of the architecture comparison by finding the paths through the graphs that maximize the pair-wise architecture similarity. In a large-scale evaluation on more than 10000 human-yeast ortholog pairs, architecture similarities assessed with FAS are consistently more plausible than those obtained using e-values to resolve overlaps or leaving overlaps unresolved. Three case studies demonstrate the utility of FAS on architecture comparison tasks: benchmarking of orthology assignment software, identification of functionally diverged orthologs, and diagnosing protein architecture changes stemming from faulty gene predictions. With the help of FAS, feature architecture comparisons can now be routinely integrated into these and many other applications. FAS is available as python package: https://pypi.org/project/greedyFAS/.

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum.

Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.

Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance to Fusarium wilt in tung tree.

The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana's resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.

Comparison and Functional Analysis of Odorant-Binding Proteins and Chemosensory Proteins in Two Closely Related Thrips Species, Frankliniella occidentalis and Frankliniella intonsa (Thysanoptera: Thripidae) Based on Antennal Transcriptome Analysis.

Two closely related thrips species, Frankliniella occidentalis and Frankliniella intonsa, are important pests on agricultural and horticultural crops. They have several similarities, including occurrence patterns, host range, and aggregation pheromone compounds. However, there are very few reports about the chemosensory genes and olfactory mechanisms in these two species. To expand our knowledge of the thrips chemosensory system, we conducted antennal transcriptome analysis of two thrips species, and identified seven odorant-binding proteins (OBPs) and eight chemosensory proteins (CSPs) in F. occidentalis, as well as six OBPs and six CSPs in F. intonsa. OBPs and CSPs showed high sequence identity between the two thrips species. The RT-qPCR results showed that the orthologous genes FoccOBP1/3/4/5/6, FintOBP1/3/4/6, FoccCSP1/2/3, and FintCSP1/2 were highly expressed in male adults. Molecular docking results suggested that orthologous pairs FoccOBP4/FintOBP4, FoccOBP6/FintOBP6, and FoccCSP2/FintCSP2 might be involved in transporting the major aggregation pheromone compound neryl (S)-2-methylbutanoate, while orthologous pairs FoccOBP6/FintOBP6, FoccCSP2/FintCSP2, and FoccCSP3/FintCSP3 might be involved in transporting the minor aggregation pheromone compound (R)-lavandulyl acetate. These results will provide a fundamental basis for understanding the molecular mechanisms of pheromone reception in the two thrips species.

RBPMS2 Is a Myocardial-Enriched Splicing Regulator Required for Cardiac Function.

RBPs (RNA-binding proteins) perform indispensable functions in the post-transcriptional regulation of gene expression. Numerous RBPs have been implicated in cardiac development or physiology based on gene knockout studies and the identification of pathogenic RBP gene mutations in monogenic heart disorders. The discovery and characterization of additional RBPs performing indispensable functions in the heart will advance basic and translational cardiovascular research. We performed a differential expression screen in zebrafish embryos to identify genes enriched in nkx2.5-positive cardiomyocytes or cardiopharyngeal progenitors compared to nkx2.5-negative cells from the same embryos. We investigated the myocardial-enriched gene RNA-binding protein with multiple splicing (variants) 2 [RBPMS2)] by generating and characterizing rbpms2 knockout zebrafish and human cardiomyocytes derived from RBPMS2-deficient induced pluripotent stem cells. We identified 1848 genes enriched in the nkx2.5-positive population. Among the most highly enriched genes, most with well-established functions in the heart, we discovered the ohnologs rbpms2a and rbpms2b, which encode an evolutionarily conserved RBP. Rbpms2 localizes selectively to cardiomyocytes during zebrafish heart development and strong cardiomyocyte expression persists into adulthood. Rbpms2-deficient embryos suffer from early cardiac dysfunction characterized by reduced ejection fraction. The functional deficit is accompanied by myofibril disarray, altered calcium handling, and differential alternative splicing events in mutant cardiomyocytes. These phenotypes are also observed in RBPMS2-deficient human cardiomyocytes, indicative of conserved molecular and cellular function. RNA-sequencing and comparative analysis of genes mis-spliced in RBPMS2-deficient zebrafish and human cardiomyocytes uncovered a conserved network of 29 ortholog pairs that require RBPMS2 for alternative splicing regulation, including RBFOX2, SLC8A1, and MYBPC3. Our study identifies RBPMS2 as a conserved regulator of alternative splicing, myofibrillar organization, and calcium handling in zebrafish and human cardiomyocytes.

Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica.

The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome assembly for apple was released and is now considered to be the reference genome. Moreover, as in several other species, the identified TCP genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the TCP gene family based on the latest genome assembly of M. × domestica. Compared to the previous classification, the number of TCP genes decreased from 52 to 40 as a result of the addition of three sequences and the deduction of 15. An analysis of the intragenic identity led to the identification of 15 pairs of orthologs, shedding light on the forces that shaped the evolution of this gene family. Furthermore, a revised nomenclature system is proposed that is based both on the intragenic identity and the homology with Arabidopsis thaliana (A. thaliana) TCPs in an effort to set a common standard for the TCP classification that will facilitate any future interspecific analysis.