Evolutionary Tree Research Articles

Identification and Characterization of EIN3/EIL Transcription Factor Family Members in Pinus massoniana Lamb.

Transcription factors refer to types of proteins that perform significant functions in the process of gene expression regulation. The ethylene insensitive 3/ethylene insensitive 3-like (EIN3/EIL) family, functioning as significant transcription factors regulating ethylene, plays a critical role in the growth and development of plants and participates in the plant’s response to diverse environmental stresses. Pinus massoniana is an excellent native tree with high economic and ecological value. However, the study of EIN3/EIL genes in gymnosperms, for instance, P. massoniana, is still relatively limited. In this research, four putative EIN3/EIL genes were identified in the transcriptome of P. massoniana. Bioinformatics analysis showed that PmEIL genes contain a highly conserved EIN3 domain and other structural features of acidic, proline-rich and glutamine-rich sites. The molecular evolution tree analysis demonstrated that the EIN3/EIL family was partitioned into three categories (A, B, and C), and the number, type, and distribution of conserved motifs grouped in one category were similar. The results of qRT-PCR indicated that the expression levels of PmEIL genes were markedly elevated in needles compared to other tissues. Through the analysis of expression patterns of the PmEIL genes under various stress treatments, it was found that the PmEIL genes could participate in plant hormone stimulation induction, osmosis, drought and other response processes. In addition, PmEIL is a nuclear localization protein. PmEIL1, PmEIL3, and PmEIL4 are transcriptional activators, while PmEIL2 is a transcriptional suppressor. This research provides a basis for further elucidating the function of EIN3/EIL transcription factors in growth, development and stress response of P. massoniana.

Spatial representation: How fish know their place

Mammalian place cells are active at one or a few specific locations in the environment. First described in the rodent hippocampus, and subsequently across the mammalian evolutionary tree, place cells have now been discovered in the larval zebrafish telencephalon.

The Evolution of NLR Inflammasome and Its Mediated Pyroptosis in Metazoa.

Nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) inflammasomes are multiprotein signaling platforms that control the inflammatory response and coordinate antimicrobial defense. In the present study, the distribution of NLR, Caspase-1, and gasdermin (GSDM) homologues and their structural characteristics and evolutionary relationships were systematically analyzed in metazoa according to the genomes of species. In invertebrates, there were only NLRC and/or NLRD presented from sponge to amphioxus, and according to the evolutionary tree, NLR from sponge located in the most primitive position. Caspase-1 existed in some metazoan phyla (Brachiopoda, Ectoprocta, Arthropoda, Mollusca, Annelia, Nematoda, Platyelminthes, Coelenterate, and Porifera) and its activation sites were relatively conserved. The amino acid sequences and three-dimensional structures of N-terminal CARD/Death domain of NLR and Caspase-1 were similar in species from sponge to human. NLR and Caspase-1 co-existed in species of Brachiopoda, Mollusca, Annelia, Coelenterate, and Porifera. There was only GSDME or PJVK found in some phyla of invertebrates and their cleavage sites were conserved (DxxD). And it was predicted that the NLR inflammasome in inducing pyroptosis could occur in species of Brachiopoda, Mollusca, Annelia, and Coelenterate. These studies indicated that NLR inflammasome emerged early in sponges of metazoa, and NLR inflammasome in inducing pyroptosis first appeared in Coelenterate, suggesting that inflammasome and its mediated pyroptosis had existed in the early stage of metazoa, but they had been lost in many species during evolution.

Cloning, sequence analysis, and functional study of the PeDof-4 gene in response to drought stress

DNA-binding with one finger (Dof) was a functionally important gene in plant stress tolerance processes. The cloned full-length (849bp) passion fruit PeDof-4 gene was sequenced, which encodes 282 amino acids with the molecular formula C1274H1983N375O408S14, molecular weight 29529.87 u, and theoretical isoelectric point pI of 8.96. Evolutionary tree analysis showed that the PeDof-4-encoded proteins had a high degree of identity with Dof-encoded proteins in other plants. Blastp of the PeDof-4 encoded proteins revealed a closer affinity to the proteins encoded by the Dof of Theobroma cacao. The relative expression of the PeDof-4 gene was higher at 50% of the relative soil moisture content in the fluorescence qPCR experiments under different levels of drought stress. Tissue-specific analysis showed that the highest expression of this gene was found in the roots. Overexpression of GUS gene under the PeDof-4 promoter inbidopsis thaliana showed that PeDof-4 could significantly respond to drought stress. Bangladesh J. Bot. 52(3): 653-663, 2024 (September) Special

Identification of the DEAD-box gene family and expression analysis of abiotic stress in potatoes

ABSTRACT Unwinding enzymes are a group of highly conserved enzymes that play important roles in plant growth and development as well as in adverse and stress conditions. The DEAD-box family represents the largest subfamily of deconjugating enzymes. However, little research has been conducted on the DEAD-box RNA gene family (StRH) in potato. Identifying and screening members of the DEAD-box gene family in potato could help us to better understand the response of potatoes to adverse and stress conditions and the related tolerance mechanisms. We identified a total of 73 DEAD-box gene family members from the potato genome-wide database. A comprehensive bioinformatics study of the potato DEAD-box family was carried out by a range of analytical methods. The evolutionary tree demonstrated that the potato DEAD-box family was divided into five distinct taxa. Three pairs of segmental repeats were identified on the chromosomes. In addition, we selected nine DEAD-box genes for qPCR(Quantitative Real-time PCR), and the results indicated that all of these genes were involved in both the ABA hormone stress and drought stress. These findings may help to increase our understanding of the functional diversity of the potato DEAD-box gene family under different environmental stresses.

Adaptations and metabolic evolution of myzozoan protists across diverse lifestyles and environments.

SUMMARYMyzozoans encompass apicomplexans and dinoflagellates that manifest diverse lifestyles in highly varied environments. They show enormous propensity to employ different metabolic programs and exploit different nutrient resources and niches, and yet, they share much core biology that underlies this evolutionary success and impact. This review discusses apicomplexan parasites of medical significance and the traits and properties they share with non-pathogenic myzozoans. These include the versatility of myzozoan plastids, which scale from fully photosynthetic organelles to the site of very select key metabolic pathways. Pivotal evolutionary innovations, such as the apical complex, have allowed myzozoans to shift from predatory to parasitic and other symbiotic lifestyles multiple times in both apicomplexan and dinoflagellate branches of the myzozoan evolutionary tree. Such traits, along with shared mechanisms for nutrient acquisition, appear to underpin the prosperity of myzozoans in their varied habitats. Understanding the mechanisms of these shared traits has the potential to spawn new strategic interventions against medically and veterinary relevant parasites within this grouping.

Transcriptome Wide Identification and Expression Analysis Revealed BhTALE Gene Family Regulates Wax Gourd (Benincasa hispida) Response to Low Calcium and Magnesium Stress

The three-amino-loop-extension (TALE) family involves key transcription factors vital for maintaining different aspects of growth including leaf, flower, and fruit development and responses to stressful stimulus. Thus far, a deep understanding of the TALE gene family in wax gourd subjected to low calcium and magnesium stress has been missing. Here, we isolated 24 BhTALE genes from a wax gourd genome database. Comprehensive bioinformatic analysis, including evolutionary tree, gene structures, conserved motifs, and chemical properties, provide structural and functional insights into the BhTALE gene family. Gene ontology (GO) analysis of TALE genes unveils their involvement in growth and stress responses. Promoter analysis indicates that hormones and stresses can influence the expression of BhTALE genes. Tissue-specific expression under low calcium and magnesium stress showed that BhTALE genes were more active in the leaves and roots. Notably, BhTALE7, BhTALE10, and BhTALE14 were expressed differentially in leaves under low calcium and magnesium applications. Similarly, the induced expression pattern of BhTALE4 was recorded in the roots under low calcium and magnesium applications. Our findings underscore the pivotal role of the BhTALE gene family in dealing with low calcium and magnesium stress in the wax gourd.

New generalized metric based on branch length distance to compare B cell lineage trees

The B cell lineage tree encapsulates the successive phases of B cell differentiation and maturation, transitioning from hematopoietic stem cells to mature, antibody-secreting cells within the immune system. Mathematically, this lineage can be conceptualized as an evolutionary tree, where each node represents a distinct stage in B cell development, and the edges reflect the differentiation pathways. To compare these lineage trees, a rigorous mathematical metric is essential. Analyzing B cell lineage trees mathematically and quantifying changes in lineage attributes over time necessitates a comparison methodology capable of accurately assessing and measuring these changes. Addressing the intricacies of multiple B cell lineage tree comparisons, this study introduces a novel metric that enhances the precision of comparative analysis. This metric is formulated on principles of metric theory and evolutionary biology, quantifying the dissimilarities between lineage trees by measuring branch length distance and weight. By providing a framework for systematically classifying lineage trees, this metric facilitates the development of predictive models that are crucial for the creation of targeted immunotherapy and vaccines. To validate the effectiveness of this new metric, synthetic datasets that mimic the complexity and variability of real B cell lineage structures are employed. We demonstrated the ability of the new metric method to accurately capture the evolutionary nuances of B cell lineages.

Occurrence and molecular characterization of Giardia spp. in snakes from China

Giardia intestinalis is a major diarrhea-causing parasite that colonizes the proximal small intestine of humans and various other mammalian species, including pets and livestock. Despite its global occurrence, there is limited information about the epidemiology of Giardia in reptiles, particularly snakes. The aim of this study was to amplify the beta-giardin (bg) gene of Giardia by polymerase chain reaction (PCR), followed by a comparative evolutionary tree analysis to determine the occurrence and molecular characterization of Giardia in snakes. We collected 603 asymptomatic samples from 26 provinces in China, representing species such as Pantherophis guttatus, Pantherophis obsoletus, Pituophis melanoleucus, Thamnophis sirtalis, Lampropeltis getula, and Heterodon nasicus. Ultimately, a occurrence of Giardia infection of 4.15 % was detected in these snakes, with corn snakes (Pantherophis guttatus) having a significantly higher occurrence than other species. Molecular analysis identified assemblage F as the predominant genotype, and also identified an assemblage B that can infect humans and a variety of mammals. The results of this study illustrate the potential risk of transmission of Giardia from snakes to humans, especially in environments where close contact occurs. The present epidemiological study examines epidemiological investigations of Giardia in reptiles, provides data to understand the zoonotic risk of Giardia, and emphasizes the need for targeted surveillance, stringent hygiene measures, and public awareness campaigns to reduce these risks.

The coevolution of fungus-ant agriculture.

Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276 ants. We found that fungus-ant agriculture originated ~66 million years ago when the end-of-Cretaceous asteroid impact temporarily interrupted photosynthesis, causing global mass extinctions but favoring the proliferation of fungi. Subsequently, ~27 million years ago, one ancestral fungal cultivar population became domesticated, i.e., obligately mutualistic, when seasonally dry habitats expanded in South America, likely isolating the cultivar population from its free-living, wet forest-dwelling conspecifics. By revealing these and other major transitions in fungus-ant coevolution, our results clarify the historical processes that shaped a model system for nonhuman agriculture.

Genomic and Transcriptional Analysis of the Necroptosis Pathway Elements RIPK and MLKL in Sea Cucumber, Holothuria leucospilota.

Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in sea cucumber remains limited. Methods: We searched the genomes of sea cucumber Holothuria leucospilota for genes encoding RIPKs and MLKL, performed phylogenetic tree, motif and functional domain analyses, and examined tissue distribution and embryonic development patterns using qPCR. Results: RIPK5 (Hl-RIPK5), RIPK7 (Hl-RIPK7) and MLKL (Hl-MLKL) were identified in sea cucumber H. leucospilota. Hl-RIPK5 and Hl-RIPK7 were mainly expressed in coelomocytes, suggesting that they play a role in innate immunity, whereas Hl-MLKL exhibited relatively low expression across tissues. During embryonic development, Hl-MLKL was highly expressed from the 2-cell stage to the morula stage, while Hl-RIPK5 and Hl-RIPK7 were primarily expressed after the morula stage, indicating different roles in embryonic development. In primary coelomocytes, Hl-RIPK5 transcriptional activity was significantly depressed by LPS, poly(I:C), or pathogen Vibrio harveyi. Hl-RIPK7 expression levels were unchanged following the same challenges. Hl-MLKL mRNA levels were significantly decreased with poly(I:C) or V. harveyi, but did not change with LPS. Conclusions: These findings provide valuable insights into the evolutionary tree and characterization of RIPK and MLKL genes in sea cucumber, contributing to the broader understanding of the RIPK gene family and MLKL in ancient echinoderms.

Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges

Significant advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7115 milk production records (milk, fat and protein yield) from 3006 cows (first 5 lactations). Since little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) cytoplasmic model with maternal lineages (CYTO), (2) haplotypic model with mitogenome sequences (HAPLO), (3) amino acid model with unique amino acid sequences (AMINO), (4) evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.

Review on the Glutinous Physiological Quality and SS Genes Polymorphism of Indian Pumpkin Germplasm Resources

Indian pumpkin, as one of the major cultivars of annual trailing herbaceous plants of the genus Pumpkin in the family Cucurbitaceae, is native to South America and widely grown in China, especially in Zhejiang Province, which is an important garden crop and food crop in China. Starch is an important component of pumpkin pulp and an important basis for the glutinous quality of pumpkin germplasm resources, and its synthesis is mainly determined by the SS (Starch synthases) gene in pumpkin. This review takes Indian pumpkin as an example to summarize the current progress of research on starch and explore its biosynthesis and regulatory processes, including the analysis of the physicochemical properties of the SS gene and the construction and analysis of the evolutionary tree, etc. Meanwhile, with the development of molecular marker technology, it has become possible to utilize bioinformatics tools to analyze the sequence and predict the physicochemical properties of the SS gene family members in Indian pumpkin, and the use of related technologies will promote pumpkin related results into life use.

Unmasking the Global Journey: Investigation of SARS-CoV-2 Variants of Interest Across Various Regions Through Whole-Genome and Phylogenetic Analysis

Background: The prolonged course of the Coronavirus Disease 2019 (COVID-19) pandemic and the virus's high mutation rate have sparked widespread interest in studying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Research has shown that SARS-CoV-2 has evolved into numerous variants since its discovery. Objectives: This study aimed to investigate the differences in SARS-CoV-2 Variants of Interest (VOI) and Variants of Concern (VOC) from different geographical regions through phylogenetic analysis and mutational analysis. Methods: A total of 700 SARS-CoV-2 whole-genome sequences were retrieved from the GISAID database from January 1, 2021, to December 31, 2021. These sequences were aligned with the reference sequence (NC_045512) using Clustal Omega version 1.2.4. A phylogenetic tree was constructed using the IQ-TREE web server and visualized using ItoL. Results: The results revealed a fully resolved maximum likelihood tree with statistical support based on bootstrap values. The analysis demonstrated that Delta variant sequences clustered separately from other VOIs, VOCs, and outgroups. The shorter topology of the Delta variant showed that Africa branched away, similar to the Lambda and Gamma variants. Additionally, structural analysis identified three primarily uniform clusters in Europe, North America, and South America, which corresponded to the sister relationships observed in Clades 1, 2, and 7 topologies. These evolutionary trees were later linked to mutations in the spike, nucleocapsid, and nsp3 proteins, which displayed a high number of mutations. Conclusions: This study provides new insights into the evolving mutations of SARS-CoV-2 VOIs and VOCs across different regions of the world, contributing to our understanding of viral pathogenicity.

Expression of Cystathionine-β-Synthase (CBS) Genes in Grape under Various Abiotic Stresses and Subcellular Localization of VvCBS27

The cystathionine-β-synthase (CBS) domain is present in the proteins of all living organisms and functions as an energy sensor, regulating protein activity through the binding capacity of its adenosine ligands. The role of the CBS gene in plant growth and development, as well as tolerance to abiotic stresses, remains largely unknown, especially in grapevine. In our study, 32 members of the CBS gene family were obtained that were distributed on 15 chromosomes. The results of the structural and evolutionary tree analyses indicated that the VvCBS gene family exhibits diverse intron-exon patterns and highly conserved motifs. Furthermore, the phylogenetic classification of the VvCBS genes revealed the presence of three subfamilies. Subcellular localization analyses showed that the VvCBS genes are mainly located in the plasma membrane region. The secondary structure of the VvCBS protein mainly consists of α-helices, extended strands, β-turns, and random coils. The VvCBS gene family exhibited four co-linear gene pairs, while the numbers for Arabidopsis thaliana and rice were 21 and 7, respectively. The promoter cis-acting element analysis revealed the presence of light-responsive, hormone-responsive, stress-responsive, and growth- and development-related elements in the VvCBS family. The expression characterization demonstrated that 12 VvCBS genes exhibited high expression levels in all grape tissues. Additionally, the RT-qPCR expression analyses showed that the 32 VvCBS exhibited different responses to a variety of abiotic stresses (cold, drought, salt), suggesting that they were functionally differentiated. VvCBS27 was cloned from ‘Pinot Noir’ of grapevine with a coding sequence of 624 bp. Subcellular localization showed that VvCBS27 protein was mainly located in the cytoplasm, cell membrane, and nucleus. This study lays a foundation for elucidating the function of grape CBS protein.

Bioinformatic and Phenotypic Analysis of AtPCP-Ba Crucial for Silique Development in Arabidopsis.

Silique development exerts significant impacts on crop yield. CRPs (Cysteine-rich peptides) can mediate cell-cell communication during plant reproduction and development. However, the functional characterization and regulatory mechanisms of CRPs in silique development remain unclear. In this study, we identified many CRP genes downstream of the CRP gene TPD1 (TAPETUM DETERMINANT1) during silique development using a microarray assay. The novel Arabidopsis thaliana pollen-borne CRPs, the PCP-Bs (for pollen coat protein B-class) gene AtPCP-Ba, along with TPD1, are essential for silique development. The AtPCP-Ba was significantly down-regulated in tpd1 flower buds but up-regulated in OE-TPD1 flower buds and siliques. The silencing of AtPCP-Ba compromised the wider silique of OE-TPD1 plants and inhibited the morphology of OE-TPD1 siliques to the size observed in the wild type. A total of 258 CRPs were identified with the bioinformatic analysis in Arabidopsis, Brassica napus, Glycine max, Oryza sativa, Sorghum bicolor, and Zea mays. Based on the evolutionary tree classification, all CRP members can be categorized into five subgroups. Notably, 107 CRP genes were predicted to exhibit abundant expression in flowers and fruits. Most cysteine-rich peptides exhibited high expression levels in Arabidopsis and Brassica napus. These findings suggested the involvement of the CRP AtPCP-Ba in the TPD1 signaling pathway, thereby regulating silique development in Arabidopsis.

Decoding Research with a Glance: The Power of Graphical Abstracts and Infographics

Background and Aims: Historically integral to science, visual elements like Darwin’s evolutionary trees have evolved with technological advancements, leading to more sophisticated and accessible visual representations. Graphical abstracts (GA) and infographics (IG) have become pivotal in enhancing the dissemination and understanding of scientific research by transforming complex data into visually engaging summaries. This review explores the evolution, impact, and design principles of these tools in scientific communication, highlighting their significance in the digital era. Methods: We did a comprehensive review of the English literature, in April 2024, from the databases of PubMed, Scopus, Embase, and Google Scholar to curate the appropriate articles related to the GA and IG related to research-publications. We have also made some representative examples of each of these two tools, using published articles in the Apollo Medicine journal. Results: The GA and IG, are the tools that not only aid in bridging the gap between scientific communities and the public but also enhance comprehension, engagement, and retention of information across diverse audiences. By utilising strategic layouts, colours, and interactive elements, they make complex information more digestible and appealing. Conclusion: This review addresses the challenges of maintaining accuracy and avoiding oversimplification in visual science communication. The future directions suggest a move towards more interactive and immersive visual experiences, emphasising the need for empirical research to optimise design and impact. GA and IG are transforming scientific communication by making research findings more accessible and engaging, fostering a better-informed public.

The immune function of TLR4-1 gene in Octopus sinensis revealed by RNAi and RNA-seq

Toll-like receptors (TLRs) are a class of conserved pattern recognition receptors (PRRs) that are crucial for initiating the innate immune response and aiding in the clearance of pathogenic organisms. Many studies have identified TLR4 as a distinctive member of the TLR family, capable of activating both the Myeloid differentiation factor 88-dependent signaling pathway (MyD88-dependent) and the TIR-domain-containing adaptor inducing IFN-β dependent signaling pathway (TRIF-dependent). Nevertheless, the role of TLR4 in Cephalopoda is still largely unexplored. To elucidate the immune function of the OsTLR4-1 gene in Octopus sinensis, the OsTLR4-1 gene was first validated and analyzed in this study. The cDNA comprises a 2475 bp ORF region, encoding 824 amino acids. Evolutionary tree analysis indicated a high homology and a close phylogenetic relationship between the Octopus sinensis and other mollusks. RNA interference (RNAi) experiments demonstrated that the expression level of OsTLR4-1 gene and its protein in the lymphocytes of the RNAi group treated with OsTLR4-1 dsRNA was extremely significantly lower than that of the blank control group and negative control group (P < 0.01), and the expression of downstream genes of OsTLR4-1, including ligand MyD88, IRAK4, TRAF6, MKK6, Hsp90, COX2, TRAF3, and RIP1, were significantly down-regulated compared to the blank and negative control group (P < 0.01). Additionally, OsTLR4-1 expression in lymphocytes was highly significantly up-regulated in the LPS-treated group compared to the blank control group (P < 0.01), while its expression was extremely significantly lower in the LPS-treated group after OsTLR4-1 interference than in the blank control group (P < 0.01). The expression of its downstream effector genes Big Defensin (Big-Def) and histone H2A.V (H2A.V) was highly significantly up-regulated in lymphocytes in the LPS-treated group compared to the blank control group (P < 0.01), while their expression in the LPS-treated group after OsTLR4-1 interference was extremely significantly lower than that in the blank control group (P < 0.01). Through comparative transcriptome analysis of the RNAi group and the blank control group, it was found that differentially expressed genes were enriched in the Toll-like receptor signaling pathway, PI3K-AKT signaling pathway, P53 signaling pathway, MAPK signaling pathway, and NF-κB signaling pathway. qRT-PCR results of key genes in these pathways revealed a decrease in all genes except IκB and Jun2 genes. This study enhances our understanding of the immune function of the TLR gene family in O. sinensis and provides a foundation for further research into innate immune signaling pathways in cephalopods.

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BackgroundSquamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.ResultsIn this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.ConclusionIn this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

Evolution of chitin-synthase in molluscs and their response to ocean acidification

Chitin-synthase (CHS) is found in most eukaryotes and has a complex evolutionary history. Research into CHS has mainly been in the context of biomineralization of mollusc shells an area of high interest due to the consequences of ocean acidification. Exploration of CHS at the genomic level in molluscs, the evolution of isoforms, their tissue distribution, and response to environmental challenges are largely unknown. Exploiting the extensive molecular resources for mollusc species it is revealed that bivalves possess the largest number of CHS genes (12–22) reported to date in eukaryotes. The evolutionary tree constructed at the class level of molluscs indicates four CHS Type II isoforms (A-D) probably existed in the most recent common ancestor, and Type II-A (Type II-A-1/Type II-A-2) and Type II-C (Type II-C-1/Type II-C-2) underwent further differentiation. Non-specific loss of CHS isoforms occurred at the class level, and in some Type II (B-D groups) isoforms the myosin head domain, which is associated with shell formation, was not preserved and highly species-specific tissue expression of CHS isoforms occurred. These observations strongly support the idea of CHS functional diversification with shell biomineralization being one of several important functions. Analysis of transcriptome data uncovered the species-specific potential of CHS isoforms in shell formation and a species-specific response to ocean acidification (OA). The impact of OA was not CHS isoform-dependent although in Mytilus, Type I-B and Type II-D gene expression was down-regulated in both M. galloprovincialis and M. coruscus. In summary, during CHS evolution the gene family expanded in bivalves generating a large diversity of isoforms with different structures and with a ubiquitous tissue distribution suggesting that chitin is involved in many biological functions. These findings provide insight into CHS evolution in molluscs and lay the foundation for research into their function and response to environmental changes.