The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

BACKGROUND

Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs).

RESULTS

De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~ 944.2 Mb (6,728 fragments, N50 = 1.067 Mb), comprising 23,598 genes (BUSCO = 93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata, including the polymorphic transmembrane clusters (PTC1 and PTC2), RADres, and other loci. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes was seen in African compared to South American lineages.

CONCLUSIONS

The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.

Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium

Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.

Molecular evolution of the hemoglobin gene family across vertebrates

Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α₂β₂) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean d_N/d_S (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.

A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3-Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation, and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.

The genome of sheep ked (Melophagus ovinus) reveals potential mechanisms underlying reproduction and narrower ecological niches

BACKGROUND

Melophagus ovinus is considered to be of great veterinary health significance. However, little is known about the information on genetic mechanisms of the specific biological characteristics and novel methods for controlling M. ovinus.

RESULTS

In total, the de novo genome assembly of M. ovinus was 188.421 Mb in size (330 scaffolds, N50 Length: 10.666 Mb), with a mean GC content of 27.74%. A total of 13,372 protein-coding genes were functionally annotated. Phylogenetic analysis indicated that the diversification of M. ovinus and Glossina fuscipes took place 72.76 Mya within the Late Cretaceous. Gene family expansion and contraction analysis revealed that M. ovinus has 65 rapidly-evolving families (26 expansion and 39 contractions) mainly involved DNA metabolic activity, transposases activity, odorant receptor 59a/67d-like, IMD domain-containing protein, and cuticle protein, etc. The universal and tightly conserved list of milk protein orthologues has been assembled from the genome of M. ovinus. Contractions and losses of sensory receptors and vision-associated Rhodopsin genes were significant in M. ovinus, which indicate that the M. ovinus has narrower ecological niches.

CONCLUSIONS

We sequenced, assembled, and annotated the whole genome sequence of M. ovinus, and launches into the preliminary genetic mechanisms analysis of the adaptive evolution characteristics of M. ovinus. These resources will provide insights to understand the biological underpinnings of this parasite and the disease control strategies.

De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

BACKGROUND

Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO₃), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species.

RESULTS

Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2-3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome.

CONCLUSIONS

Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO₃ resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.

Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress

BACKGROUND

Calcineurin B-like proteins (CBLs) are ubiquitous Ca²⁺ sensors that mediate plant responses to various stress and developmental processes by interacting with CBL-interacting protein kinases (CIPKs). CBLs and CIPKs play essential roles in acclimatization of crop plants. However, evolution of these two gene families in the genus Medicago is poorly understood.

RESULTS

A total of 68 CBL and 135 CIPK genes have been identified in five genomes from Medicago. Among these genomes, the gene number of CBLs and CIPKs shows no significant difference at the haploid genome level. Phylogenetic and comprehensive characteristic analyses reveal that CBLs and CIPKs are classified into four clades respectively, which is validated by distribution of conserved motifs. The synteny analysis indicates that the whole genome duplication events (WGDs) have contributed to the expansion of both families. Expression analysis demonstrates that two MsCBLs and three MsCIPKs are specifically expressed in roots, mature leaves, developing flowers and nitrogen fixing nodules of Medicago sativa spp. sativa, the widely grown tetraploid species. In particular, the expression of these five genes was highly up-regulated in roots when exposed to salt and drought stress, indicating crucial roles in stress responses.

CONCLUSIONS

Our study leads to a comprehensive understanding of evolution of CBL and CIPK gene families in Medicago, but also provides a rich resource to further address the functions of CBL-CIPK complexes in cultivated species and their closely related wild relatives.

Molecular response and evolution of plant anion transport systems to abiotic stress

We propose that anion channels are essential players for green plants to respond and adapt to the abiotic stresses associated changing climate via reviewing the literature and analyzing the molecular evolution, comparative genetic analysis, and bioinformatics analysis of the key anion channel gene families. Climate change-induced abiotic stresses including heatwave, elevated CO₂, drought, and flooding, had a major impact on plant growth in the last few decades. This scenario could lead to the exposure of plants to various stresses. Anion channels are confirmed as the key factors in plant stress responses, which exist in the green lineage plants. Numerous studies on anion channels have shed light on their protein structure, ion selectivity and permeability, gating characteristics, and regulatory mechanisms, but a great quantity of questions remain poorly understand. Here, we review function of plant anion channels in cell signaling to improve plant response to environmental stresses, focusing on climate change related abiotic stresses. We investigate the molecular response and evolution of plant slow anion channel, aluminum-activated malate transporter, chloride channel, voltage-dependent anion channel, and mechanosensitive-like anion channel in green plant. Furthermore, comparative genetic and bioinformatic analysis reveal the conservation of these anion channel gene families. We also discuss the tissue and stress specific expression, molecular regulation, and signaling transduction of those anion channels. We propose that anion channels are essential players for green plants to adapt in a diverse environment, calling for more fundamental and practical studies on those anion channels towards sustainable food production and ecosystem health in the future.

Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants

Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.

A subfunctionalisation model of gene family evolution predicts balanced tree shapes

We consider a subfunctionalisation model of gene family evolution. A family of n genes that perform z functions is represented by an n×z binary matrix Y_t where a 1 in the ijth position indicates that gene i can perform function j. Y_t evolves according to a continuous time Markov chain (CTMC) that represents the processes of gene duplication, coding region loss and regulatory region loss with the restriction that each function is protected by selection, meaning that each column in the matrix must contain at least one 1. We generate gene trees based on the CTMC {Y_t,t⩾0}. We analyse the long-run behaviour of the model and specify the conditions where we expect gene trees to continue to grow and where we expect them to have a stable number of genes. We show that different choices of rate parameters for the processes of duplication and loss lead to different tree shapes as measured by two common tree-shape statistics: the β-statistic for measuring tree balance and the γ-statistic for assessing diversification rate. We use an extension of β that is estimated from sets of trees. This extension is less biased compared to using the average β value for individual trees. When the rate of gene duplication dominates the rate of gene loss, the process is unstable and the distribution of tree shapes is close to following the uniform ranked tree shape (URT) distribution. However, when the process is stable, gene trees are predicted to have positive values of β indicating balanced trees and negative values of γ indicating that diversification occurs more towards the root of the tree. The results of our analyses suggest that comparing the tree-shape statistics of empirical gene-trees to the predictions presented here will provide a test of the subfunctionalisation model.

Pathogenesis-related protein 1 (PR-1) genes in soybean: Genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions. Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups. GmPR-1 genes are under strong purifying selection, particularly those that emerged by tandem duplications. GmPR-1 promoter regions are abundant in cis-regulatory elements associated with major stress-related transcription factor families, namely WRKY, ERF, HD-Zip, C2H2, NAC, and GATA. We observed that 23 GmPR-1 genes are induced by stress conditions or exclusively expressed upon stress. We explored 1972 transcriptome samples, including 26 stress conditions, revealing that most GmPR-1 genes are differentially expressed in a plethora of biotic and abiotic stresses. Our findings highlight stress-responsive GmPR-1 genes with potential biotechnological applications, such as the development of transgenic lines with increased resistance to biotic and abiotic stresses.

Pathogenesis-related protein 1 (PR-1) genes in soybean: Genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions. Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups. GmPR-1 genes are under strong purifying selection, particularly those that emerged by tandem duplications. GmPR-1 promoter regions are abundant in cis-regulatory elements associated with major stress-related transcription factor families, namely WRKY, ERF, HD-Zip, C2H2, NAC, and GATA. We observed that 23 GmPR-1 genes are induced by stress conditions or exclusively expressed upon stress. We explored 1972 transcriptome samples, including 26 stress conditions, revealing that most GmPR-1 genes are differentially expressed in a plethora of biotic and abiotic stresses. Our findings highlight stress-responsive GmPR-1 genes with potential biotechnological applications, such as the development of transgenic lines with increased resistance to biotic and abiotic stresses.

Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL

Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.

Evolution of the DAN gene family in vertebrates

The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

Comparative and functional genomics of the ABC transporter superfamily across arthropods

BACKGROUND

The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited.

RESULTS

Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation.

CONCLUSIONS

We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.

Metalloid hazards: From plant molecular evolution to mitigation strategies

Metalloids such as boron and silicon are key elements for plant growth and crop productivity. However, toxic metalloids such as arsenic are increasing in the environment due to inputs from natural sources and human activities. These hazardous metalloids can cause serious health risks to humans and animals if they enter the food chain. Plants have developed highly regulated mechanisms to alleviate the toxicity of metalloids during their 500 million years of evolution. A better understanding the molecular mechanisms underlying the transport and detoxification of toxic metalloids in plants will shed light on developing mitigation strategies. Key transporters and regulatory proteins responsive to toxic metalloids have been identified through evolutionary and molecular analyses. Moreover, knowledge of the regulatory proteins and their pathways can be used in the breeding of crops with lower accumulation of metalloids. These findings can also assist phytoremediation by the exploration of plants such as fern species that hyperaccumulate metalloids from soils and water, and can be used to engineer plants with elevated uptake and storage capacity of toxic metalloids. In summary, there are solutions to remediate contamination due to toxic metalloids by combining the research advances and industrial technologies with agricultural and environmental practices.

Evolution of the codling moth pheromone via an ancient gene duplication

BACKGROUND

Defining the origin of genetic novelty is central to our understanding of the evolution of novel traits. Diversification among fatty acid desaturase (FAD) genes has played a fundamental role in the introduction of structural variation in fatty acyl derivatives. Because of its central role in generating diversity in insect semiochemicals, the FAD gene family has become a model to study how gene family expansions can contribute to the evolution of lineage-specific innovations. Here we used the codling moth (Cydia pomonella) as a study system to decipher the proximate mechanism underlying the production of the ∆8∆10 signature structure of olethreutine moths. Biosynthesis of the codling moth sex pheromone, (E8,E10)-dodecadienol (codlemone), involves two consecutive desaturation steps, the first of which is unusual in that it generates an E9 unsaturation. The second step is also atypical: it generates a conjugated diene system from the E9 monoene C12 intermediate via 1,4-desaturation.

RESULTS

Here we describe the characterization of the FAD gene acting in codlemone biosynthesis. We identify 27 FAD genes corresponding to the various functional classes identified in insects and Lepidoptera. These genes are distributed across the C. pomonella genome in tandem arrays or isolated genes, indicating that the FAD repertoire consists of both ancient and recent duplications and expansions. Using transcriptomics, we show large divergence in expression domains: some genes appear ubiquitously expressed across tissue and developmental stages; others appear more restricted in their expression pattern. Functional assays using heterologous expression systems reveal that one gene, Cpo_CPRQ, which is prominently and exclusively expressed in the female pheromone gland, encodes an FAD that possesses both E9 and ∆8∆10 desaturation activities. Phylogenetically, Cpo_CPRQ clusters within the Lepidoptera-specific ∆10/∆11 clade of FADs, a classic reservoir of unusual desaturase activities in moths.

CONCLUSIONS

Our integrative approach shows that the evolution of the signature pheromone structure of olethreutine moths relied on a gene belonging to an ancient gene expansion. Members of other expanded FAD subfamilies do not appear to play a role in chemical communication. This advises for caution when postulating the consequences of lineage-specific expansions based on genomics alone.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

Stage-specific transcriptomic analysis of the model cestode Hymenolepis microstoma

Most parasitic flatworms go through different life stages with important physiological and morphological changes. In this work, we used a transcriptomic approach to analyze the main life-stages of the model tapeworm Hymenolepis microstoma (eggs, cysticercoids, and adults). Our results showed massive transcriptomic changes in this life cycle, including key gene families that contribute substantially to the expression load in each stage. In particular, different members of the cestode-specific hydrophobic ligand-binding protein (HLBP) family are among the most highly expressed genes in each life stage. We also found the transcriptomic signature of major metabolic changes during the transition from cysticercoids to adult worms. Thus, this work contributes to uncovering the gene expression changes that accompany the development of this important cestode model species, and to the best of our knowledge represents the first transcriptomic study with robust replicates spanning all of the main life stages of a tapeworm.

Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

Background

Nematodes have evolved to survive in diverse ecological niches and can be a serious burden on agricultural economy, veterinary medicine, and public health. Antioxidant enzymes in parasitic nematodes play a critical role in defending against host oxidative stress. However, the features of the evolution of antioxidant enzymes in the phylum Nematoda remain elusive.

Results

Here, we systematically investigated the evolution and gene expression of antioxidant enzymes in the genomes of 59 nematodes and transcriptomes of 20 nematodes. Catalase has been independently lost in several orders, suggesting that it is unnecessary for some nematodes. Unlike in mammals, phospholipid hydroperoxide glutathione peroxidase is widely distributed in nematodes, among which it has evolved independently. We found that superoxide dismutase (SOD) has been present throughout nematode evolutionary process, and the extracellular isoform (SOD3) is diverged from the corresponding enzyme in mammals and has undergone duplication and differentiation in several nematodes. Moreover, the evolution of intracellular and extracellular SOD isoforms in filaria strongly indicates that extracellular SOD3 originated from intracellular SOD1 and underwent rapid evolution to form the diversity of extracellular SOD3. We identify a novel putative metal-independent extracellular SOD presenting independently in Steinernema and Strongyloididae lineage that featured a high expression level in Strongyloides larvae. Sequence divergence of SOD3 between parasitic nematodes and their closest free-living nematode, the specifically high expression in the parasitic female stage, and presence in excretory-secretory proteome of Strongyloides suggest that SOD3 may be related with parasitism.

Conclusions

This study advances our understanding of the complex evolution of antioxidant enzymes across Nematoda and provides targets for controlling parasitic nematode diseases.

The rise and fall of globins in the amphibia

The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented α^D-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.

Understanding aquaporin transport system in highly stress-tolerant and medicinal plant species Jujube (Ziziphus jujuba Mill.)

Jujube (Ziziphus jujubaMill.), a deciduous tree, is well known for its medicinal and nutritional values. Being an extremophile, it has an excellent capability to survive under arid conditions with limited water availability. In this regard, studying the role of water transport regulating proteins such as Aquaporins (AQPs) in jujube is of great importance. Aquaporins, channel-forming proteins are known to have a significant role in the transport of water and many other small solutes in plants. In the present study, computational approaches have identified 36 AQPs, which comprised of 12 NIPs (Nodulin 26-like intrinsic proteins), 10 PIPs (Plasma membrane intrinsic proteins), 10 TIPs (Tonoplast intrinsic proteins), 3 SIPs (Small intrinsic proteins), and 1 XIP (uncharacterized intrinsic protein). Conserved features of AQPs like asparagines-proline-alanine (NPA) amino acid motifs, aromatic/arginine (ar/R) selectivity filters, and Frogger's residues, having a significant role in solute specificity and transport, were also predicted. Homology-based tertiary (3D) structures of AQP_S were also resolved using various tools, and subsequently, pore-lining residues have been identified using the 3D structures. The information of pore morphology, along with the conserved features provided through this work, will be helpful to predict solute specificity of AQPs. Analysis of transcriptomic data revealed the tissue-specific or ubiquitous expression of several AQPs in different tissues of jujube. Interestingly, TIP3-1 was found to have fruit specific expression whereas most of the AQPs have a relatively low expression. Based on the present study and previous reports, TIP3s seems to have a significant role in seed desiccation processes. The findings presented here provide pivotal insights into the functions of extremophile specific AQPs, to better understand the role of AQPs and, subsequently, the stress tolerance mechanism in jujube.

Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds

Background

ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds.

Results

We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution.

Conclusions

We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.

The evolution of ADAM gene family in eukaryotes

The ADAM (A Disintegrin And Metalloprotease) gene family encodes proteins with adhesion and proteolytic functions. ADAM proteins are associated with diseases like cancers. Twenty ADAM genes have been identified in humans. However, little is known about the evolution of the family. We analyzed the repertoire of ADAM genes in a vast number of eukaryotic genomes to clarify the main gene copy number expansions. For the first time, we provide compelling evidence that early-branching green algae (Mamiellophyceae) have ADAM genes, suggesting that they originated in the last common ancestor of eukaryotes, before the split of plants, fungi and animals. The ADAM family expanded in early metazoans, with the most significative gene expansion happening during the first steps of vertebrate evolution. We concluded that most of mammal ADAM diversity can be explained by gene duplications in early bone fish. Our data suggest that ADAM genes were lost early in green plant evolution.

Trait differentiation and modular toxin expression in palm-pitvipers

Background

Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A₂ (PLA₂) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis nigroviridis) and Talamancan Palm-Pitvipers (B. nubestris).

Results

We assembled 1517 coding sequences, including 43 toxins for B. nigroviridis and 1787 coding sequences including 42 toxins for B. nubestris. The venom gland transcriptomes were extremely divergent between these two species with one B. nigroviridis exhibiting a primarily neurotoxic pattern of expression, both B. nubestris expressing primarily hemorrhagic toxins, and a second B. nigroviridis exhibiting a mixed expression phenotype. Weighted gene coexpression analyses identified six submodules of transcript expression variation, one of which was highly associated with SVMPs and a second which contained both subunits of the neurotoxic PLA₂ complex. The sub-module association of these toxins suggest common regulatory pathways underlie the variation in their expression and is consistent with known patterns of inheritance of similar haplotypes in other species. We also find evidence that module associated toxin families show fewer gene duplications and transcript losses between species, but module association did not appear to affect sequence diversification.

Conclusion

Sub-modular regulation of expression likely contributes to the diversification of venom phenotypes within and among species and underscores the role of modularity in facilitating rapid evolution of complex traits.

On the Evolution and Functional Diversity of Terpene Synthases in the Pinus Species: A Review

In the biosynthesis of terpenoids, the ample catalytic versatility of terpene synthases (TPS) allows the formation of thousands of different molecules. A steadily increasing number of sequenced plant genomes invariably show that the TPS gene family is medium to large in size, comprising from 30 to 100 functional members. In conifers, TPSs belonging to the gymnosperm-specific TPS-d subfamily produce a complex mixture of mono-, sesqui-, and diterpenoid specialized metabolites, which are found in volatile emissions and oleoresin secretions. Such substances are involved in the defence against pathogens and herbivores and can help to protect against abiotic stress. Oleoresin terpenoids can be also profitably used in a number of different fields, from traditional and modern medicine to fine chemicals, fragrances, and flavours, and, in the last years, in biorefinery too. In the present work, after summarizing the current views on the biosynthesis and biological functions of terpenoids, recent advances on the evolution and functional diversification of plant TPSs are reviewed, with a focus on gymnosperms. In such context, an extensive characterization and phylogeny of all the known TPSs from different Pinus species is reported, which, for such genus, can be seen as the first effort to explore the evolutionary history of the large family of TPS genes involved in specialized metabolism. Finally, an approach is described in which the phylogeny of TPSs in Pinus spp. has been exploited to isolate for the first time mono-TPS sequences from Pinus nigra subsp. laricio, an ecologically important endemic pine in the Mediterranean area.

The power of neuropeptide precursor sequences to reveal phylogenetic relationships in insects: A case study on Blattodea

Recent state-of-the-art analyses in insect phylogeny have exclusively used very large datasets to elucidate higher-level phylogenies. We have tested an alternative and novel approach by evaluating the potential phylogenetic signals of identified and relatively short neuropeptide precursor sequences with highly conserved functional units. For that purpose, we examined available transcriptomes of 40 blattodean species for the translated amino acid sequences of 17 neuropeptide precursors. Recently proposed intra-ordinal relationships of Blattodea, based on the analysis of 2370 protein-coding nuclear single-copy genes (Evangelista et al., 2019), were corroborated with maximum support. The functionally different precursor units were analyzed separately for their phylogenetic information. Although the degree of information was different in the different sequence motifs, all precursor units contained phylogenetic informative data at the ordinal level, and their separate analysis did not reveal contradictory topologies. This study is the first comprehensive exploitation of complete neuropeptide precursor sequences of arthropods in such a context and demonstrates the applicability of these rather short but conserved sequences for an alternative, fast and simple analysis of phylogenetic relationships.

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata

BACKGROUND

Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.

RESULTS

A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.

CONCLUSIONS

The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

BACKGROUND

The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.

RESULTS

We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.

CONCLUSIONS

Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

BACKGROUND

The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS

The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS

With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

BACKGROUND

The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS

The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS

With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues

Background

Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.

Results

We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult C. gigantea. In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between C. gigantea and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to C. gigantea, and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members.

Conclusions

This study presents the first comprehensive transcriptome characterization of C. gigantea. Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5584-6) contains supplementary material, which is available to authorized users.

MIPhy: identify and quantify rapidly evolving members of large gene families

After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions. These can be identified by analyzing the gene family across several species and identifying patterns of gene duplication and loss that do not correlate with the known relationships between those species. This signature, termed phylogenetic instability, has been previously linked to adaptations that change the way an organism samples and responds to its environment; conversely, low phylogenetic instability has been previously linked to proteins with endogenous functions. With the increase in genome-level data, there is a need to identify and quantify phylogenetic instability. Here, we present Minimizing Instability in Phylogenetics (MIPhy), a tool that solves this problem by quantifying the incongruence of a gene's evolutionary history. The motivation behind MIPhy was to produce a tool to aid in interpreting phylogenetic trees. It can predict which members of a gene family are under adaptive evolution, working only from a gene tree and the relationship between the species under consideration. While it does not conduct any estimation of positive selection-which is the typical indication of adaptive evolution-the results tend to agree. We demonstrate the usefulness of MIPhy by accurately predicting which members of the mammalian cytochrome P450 gene superfamily metabolize xenobiotics and which metabolize endogenous compounds. Our predictions correlate very well with known substrate specificities of the human enzymes. We also analyze the Caenorhabditis collagen gene family and use MIPhy to predict genes that produce an observable phenotype when knocked down in C. elegans, and show that our predictions correlate well with existing knowledge. The software can be downloaded and installed from https://github.com/dave-the-scientist/miphy and is also available as an online web tool at http://www.miphy.wasmuthlab.org.

New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants

The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research.

Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD₁ class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD₂ group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g., DRD_2l and DRD_4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D₁ class of dopamine receptors and the time of origin of the DRD_2l and DRD_4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD₁ group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD₁ class of dopamine receptors we recovered the sister group relationship between the DRD_1C and DRD_1E, and this clade was recovered sister to a cyclostome sequence. The DRD₁ clade was recovered sister to the aforementioned clade, and the group containing DRD₅ receptors was sister to all other DRD₁ paralogs. In agreement with the literature, among the DRD₂ class of receptors, DRD₂ was recovered sister to DRD₃, whereas DRD₄ was sister to the DRD₂/DRD₃ clade. According to our phylogenetic tree, the DRD_2l and DRD_4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.

Polyamines in the life of Arabidopsis: profiling the expression of S-adenosylmethionine decarboxylase (SAMDC) gene family during its life cycle

BACKGROUND

Arabidopsis has 5 paralogs of the S-adenosylmethionine decarboxylase (SAMDC) gene. Neither their specific role in development nor the role of positive/purifying selection in genetic divergence of this gene family is known. While some data are available on organ-specific expression of AtSAMDC1, AtSAMDC2, AtSAMDC3 and AtSAMDC4, not much is known about their promoters including AtSAMDC5, which is believed to be non-functional.

RESULTS

(1) Phylogenetic analysis of the five AtSAMDC genes shows similar divergence pattern for promoters and coding sequences (CDSs), whereas, genetic divergence of 5'UTRs and 3'UTRs was independent of the promoters and CDSs; (2) while AtSAMDC1 and AtSAMDC4 promoters exhibit high activity (constitutive in the former), promoter activities of AtSAMDC2, AtSAMDC3 and AtSAMDC5 are moderate to low in seedlings (depending upon translational or transcriptional fusions), and are localized mainly in the vascular tissues and reproductive organs in mature plants; (3) based on promoter activity, it appears that AtSAMDC5 is both transcriptionally and translationally active, but based on it's coding sequence it seems to produce a non-functional protein; (4) though 5'-UTR based regulation of AtSAMDC expression through upstream open reading frames (uORFs) in the 5'UTR is well known, no such uORFs are present in AtSAMDC4 and AtSAMDC5; (5) the promoter regions of all five AtSAMDC genes contain common stress-responsive elements and hormone-responsive elements; (6) at the organ level, the activity of AtSAMDC enzyme does not correlate with the expression of specific AtSAMDC genes or with the contents of spermidine and spermine.

CONCLUSIONS

Differential roles of positive/purifying selection were observed in genetic divergence of the AtSAMDC gene family. All tissues express one or more AtSAMDC gene with significant redundancy, and concurrently, there is cell/tissue-specificity of gene expression, particularly in mature organs. This study provides valuable information about AtSAMDC promoters, which could be useful in future manipulation of crop plants for nutritive purposes, stress tolerance or bioenergy needs. The AtSAMDC1 core promoter might serve the need of a strong constitutive promoter, and its high expression in the gametophytic cells could be exploited, where strong male/female gametophyte-specific expression is desired; e.g. in transgenic modification of crop varieties.

Progressive erosion of the Relaxin1 gene in bovids

The relaxin/insulin-like (RLN/INSL) gene family is a group of genes that encode peptide hormones involved in a variety of physiological functions related to reproduction. Previous studies have shown that relaxin plays a key role in widening of the pubic bone during labor and in gamete maturation. Because of these functions, studying the evolution of RLN1, the gene encoding for relaxin, is relevant in livestock species, most of which belong in the group Laurasiatheria, which includes cow, pig, horse, goat, and sheep in addition to bats, cetaceans and carnivores. Experimental evidence suggests that cows do not synthesize relaxin, but respond to it, and sheep apparently have a truncated RLN1 gene. Thus, we made use of genome sequence data to characterize the genomic locus of the RLN1 gene in Laurasiatherian mammals to better understand how cows lost the ability to synthesize this peptide. We found that all ruminants in our study (cow, giraffe, goat, sheep and Tibetan antelope) lack a functional RLN1 gene, and document the progressive loss of RLN1 in the lineage leading to cows. Our analyses indicate that 1 - all ruminants have lost all key regulatory elements upstream of the first exon, 2 - giraffe, goat, sheep and Tibetan antelope have multiple inactivating mutations in the RLN1 pseudogene, and 3 - the cow genome has lost all traces of RLN1. The 5' regulatory sequence plays a key role in activating expression, and the loss of this sequence would impair synthesis of mRNA. Our results suggest that changes in regulatory sequence preceded mutations in coding sequence and highlight the importance of these regions in maintaining proper gene function. In addition, we found that all bovids examined posses copies of the relaxin receptors, which explains why they are able to respond to relaxin despite their inability to produce it.

Evolution of the α2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles

Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α₂-Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α₂-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α₂-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α₂-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α₂-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α₂-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.

Genome-wide comparative analysis of putative Pth11-related G protein-coupled receptors in fungi belonging to Pezizomycotina

Background

G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi, where they play important roles in signal transduction. Among them, the Pth11-related GPCRs form a large and divergent protein family, and are only found in fungi in Pezizomycotina. However, the evolutionary process and potential functions of Pth11-related GPCRs remain largely unknown.

Results

Twenty genomes of fungi in Pezizomycotina covering different nutritional strategies were mined for putative Pth11-related GPCRs. Phytopathogens encode much more putative Pth11-related GPCRs than symbionts, saprophytes, or entomopathogens. Based on the phylogenetic tree, these GPCRs can be divided into nine clades, with each clade containing fungi in different taxonomic orders. Instead of fungi from the same order, those fungi with similar nutritional strategies were inclined to share orthologs of putative Pth11-related GPCRs. Most of the CFEM domain-containing Pth11-related GPCRs, which were only included in two clades, were detected in phytopathogens. Furthermore, many putative Pth11-related GPCR genes of phytopathogens were upregulated during invasive plant infection, but downregulated under biotic stress. The expressions of putative Pth11-related GPCR genes of saprophytes and entomopathogens could be affected by nutrient conditions, especially the carbon source. The gene expressions revealed that Pth11-related GPCRs could respond to biotic/abiotic stress and invasive plant infection with different expression patterns.

Conclusion

Our results indicated that the Pth11-related GPCRs existed before the diversification of Pezizomycotina and have been gained and/or lost several times during the evolutionary process. Tandem duplications and trophic variations have been important factors in this evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1076-5) contains supplementary material, which is available to authorized users.

Isometric gene tree reconciliation revisited

BACKGROUND

Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by Ma et al. in 2008 in the context of reconstructing evolutionary histories of genomes in the infinite sites model.

RESULTS

In this paper, we show that the original algorithm by Ma et al. is incorrect, and we propose a modified algorithm that addresses the problems that we discovered. We have also improved the running time from [Formula: see text] to [Formula: see text], where N is the total number of nodes in the two input trees. Finally, we examine two new variants of the problem: reconciliation of two unrooted trees and scaling of branch lengths of the gene tree during reconciliation of two rooted trees.

CONCLUSIONS

We provide several new algorithms for isometric reconciliation of trees. Some questions in this area remain open; most importantly extensions of the problem allowing for imprecise estimates of branch lengths.

House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity

BACKGROUND

Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution.

RESULTS

We discovered at least 47 latrotoxin genes in the house spider genome, many of which are tandem-arrayed. Latrotoxins vary extensively in predicted structural domains and expression, implying their significant functional diversification. Phylogenetic analyses show latrotoxins have substantially duplicated after the Latrodectus/Parasteatoda split and that they are also related to proteins found in endosymbiotic bacteria. Latrodectin genes are less numerous than latrotoxins, but analyses show their recruitment for venom function from neuropeptide hormone genes following duplication, inversion and domain truncation. While latrodectins and other peptides are highly expressed in house spider and black widow venom glands, latrotoxins account for a far smaller percentage of house spider venom gland expression.

CONCLUSIONS

The house spider genome sequence provides novel insights into the evolution of venom toxins once considered unique to black widows. Our results greatly expand the size of the latrotoxin gene family, reinforce its narrow phylogenetic distribution, and provide additional evidence for the lateral transfer of latrotoxins between spiders and bacterial endosymbionts. Moreover, we strengthen the evidence for the evolution of latrodectin venom genes from the ecdysozoan Ion Transport Peptide (ITP)/Crustacean Hyperglycemic Hormone (CHH) neuropeptide superfamily. The lower expression of latrotoxins in house spiders relative to black widows, along with the absence of a vertebrate-targeting α-latrotoxin gene in the house spider genome, may account for the extreme potency of black widow venom.

Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Background

The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.

Results

The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.

Conclusions

The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1049-2) contains supplementary material, which is available to authorized users.

Evolutionary history of the reprimo tumor suppressor gene family in vertebrates with a description of a new reprimo gene lineage

Genes related to human diseases should be natural targets for evolutionary studies, since they could provide clues regarding the genetic bases of pathologies and potential treatments. Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest. These genes, especially the reprimo duplicate located on human chromosome 2, have been associated with epigenetic modifications correlated with transcriptional silencing and cancer progression. We demonstrate the presence of a third reprimo lineage that, together with the reprimo and reprimo-like genes, appears to have been differentially retained during the evolutionary history of vertebrates. We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor of vertebrates. The reprimo gene has been lost in birds, and the third reprimo gene lineage has been retained in only a few distantly related species, such as coelacanth and gar. Expression analyses revealed that the reprimo paralogs are mainly expressed in the nervous system. Different vertebrate lineages have retained different reprimo paralogs, and even in species that have retained multiple copies, only one of them is heavily expressed.

Utility of the Amborella trichopoda expansin superfamily in elucidating the history of angiosperm expansins

Expansins form a superfamily of plant proteins that assist in cell wall loosening during growth and development. The superfamily is divided into four families: EXPA, EXPB, EXLA, and EXLB (Sampedro and Cosgrove in Genome Biol 6:242, 2005. doi: 10.1186/gb-2005-6-12-242 ). Previous studies on Arabidopsis, rice, and Populus trichocarpa have clarified the evolutionary history of expansins in angiosperms (Sampedro et al. in Plant J 44:409-419, 2005. doi: 10.1111/j.1365-313X.2005.02540.x ). Amborella trichopoda is a flowering plant that diverged very early. Thus, it is a sister lineage to all other extant angiosperms (Amborella Genome Project in 342:1241089, 2013. doi: 10.1126/science.1241089 ). Because of this relationship, comparing the A. trichopoda expansin superfamily with those of other flowering plants may indicate which expansin genes were present in the last common ancestor of all angiosperms. The A. trichopoda expansin superfamily was assembled using BLAST searches with angiosperm expansin queries. The search results were analyzed and annotated to isolate the complete A. trichopoda expansin superfamily. This superfamily is similar to other angiosperm expansin superfamilies, but is somewhat smaller. This is likely because of a lack of genome duplication events (Amborella Genome Project 2013). Phylogenetic and syntenic analyses of A. trichopoda expansins have improved our understanding of the evolutionary history of expansins in angiosperms. Nearly all of the A. trichopoda expansins were placed into an existing Arabidopsis-rice expansin clade. Based on the results of phylogenetic and syntenic analyses, we estimate there were 12-13 EXPA genes, 2 EXPB genes, 1 EXLA gene, and 2 EXLB genes in the last common ancestor of all angiosperms.

Calcium-dependent protein kinases in plants: evolution, expression and function

Calcium-dependent protein kinases (CPKs) are plant proteins that directly bind calcium ions before phosphorylating substrates involved in metabolism, osmosis, hormone response and stress signaling pathways. CPKs are a large multigene family of proteins that are present in all plants studied to date, as well as in protists, oomycetes and green algae, but are not found in animals and fungi. Despite the increasing evidence of the importance of CPKs in developmental and stress responses from various plants, a comprehensive genome-wide analysis of CPKs from algae to higher plants has not been undertaken. This paper describes the evolution of CPKs from green algae to plants using a broadly sampled phylogenetic analysis and demonstrates the functional diversification of CPKs based on expression and functional studies in different plant species. Our findings reveal that CPK sequence diversification into four major groups occurred in parallel with the terrestrial transition of plants. Despite significant expansion of the CPK gene family during evolution from green algae to higher plants, there is a high level of sequence conservation among CPKs in all plant species. This sequence conservation results in very little correlation between CPK evolutionary groupings and functional diversity, making the search for CPK functional orthologs a challenge.

Distribution and evolution of het gene homologs in the basidiomycota

In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.

The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities

Plant S1-like nucleases, often referred to as nuclease I enzymes, are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death. The catalytically active site of these enzymes shows a significant similarity to the well-described P1 nuclease from Penicillium citrinum. Previously published studies reported that plant S1-like nucleases possess catalytic activities similar to their fungal orthologs, i.e. they hydrolyze single-stranded DNA and RNA, and less efficiently double-stranded DNA, in the presence of zinc ions. Here we describe a comprehensive study of the nucleolytic activities of all Arabidopsis S1-like paralogs. Our results revealed that different members of this family are characterized by a surprisingly large variety of catalytic properties. We found that, in addition to Zn(2+)-dependent enzymes, this family also comprises nucleases activated by Ca(2+) and Mn(2+), which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Moreover, particular members of this class differ in their optimum pH value and substrate specificity. These results shed new light on the widely accepted classification of plant nucleases which is based on the assumption that the catalytic requirements of plant nucleases reflect their phylogenetic origin. Our results imply the need to redefine the understanding of the term 'nuclease I'. Analysis of the phylogenetic relationships between S1-like enzymes shows that plant representatives of this family evolve toward an increase in catalytic diversity. The importance of this process for the biological functions of plant S1-type enzymes is discussed.