Molecular Evolutionary Studies Research Articles

Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) upsurge sprang up in Wuhan, China, in late December 2019. Due to the exceptionally high mutation frequency, comparative genomics of viruses isolated throughout time and in various geographical locations are crucial. To better understand how SARS-CoV-2 heterogeneity has changed around the globe, this research was conducted. Nucleotide and protein sequences of SARS-CoV-2, SARS-CoV, and bat SARS-like CoV were extracted from the NCBI Virus database. The Wuhan SARS-CoV-2 variant was used as a reference. Molecular Evolutionary Genetics Study performed the phylogenetic analysis, while the Genome Detective Coronavirus Typing Tool performed the mutational analysis. The evolutionary research has revealed that bats are the primary host for coronavirus evolution and the origin of the formation of SARS-CoV and SARS-CoV-2. Numerous mutations have been discovered in the spike, envelope, and nucleocapsid protein. The current research findings may have an implication that facilitates the development of prospective immunization candidates/small pharmacological compounds targeting COVID-19.

Characteristics and Comparative Analysis of Seven Complete Plastomes of Trichoglottis s.l. (Aeridinae, Orchidaceae).

Trichoglottis exhibits a range of rich variations in colors and shapes of flower and is a valuable ornamental orchid genus. The genus Trichoglottis has been expanded by the inclusion of Staurochilus, but this Trichoglottis sensu lato (s.l.) was recovered as a non-monophyletic genus based on molecular sequences from one or a few DNA regions. Here, we present phylogenomic data sets, incorporating complete plastome sequences from seven species (including five species sequenced in this study) of Trichoglottis s.l. (including two species formerly treated as Staurochilus), to compare plastome structure and to reconstruct the phylogenetic relationships of this genus. The seven plastomes possessed the typical quadripartite structure of angiosperms and ranged from 149,402 bp to 149,841 bp with a GC content of 36.6-36.7%. These plastomes contain 120 genes, which comprise 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, all ndh genes were pseudogenized or lost. A total of 98 (T. philippinensis) to 134 (T. ionosma) SSRs and 33 (T. subviolacea) to 46 (T. ionosma) long repeats were detected. The consistent and robust phylogenetic relationships of Trichoglottis were established using a total of 25 plastid genomes from the Aeridinae subtribe. The genus Trichoglottis s.l. was strongly supported as a monophyletic group, and two species formerly treated as Staurochilus were revealed as successively basal lineages. In addition, five mutational hotspots (trnNGUU-rpl32, trnLUAA, trnSGCU-trnGUCC, rbcL-accD, and trnTGGU-psbD) were identified based on the ranking of PI values. Our research indicates that plastome data is a valuable source for molecular identification and evolutionary studies of Trichoglottis and its related genera.

Complete mitochondrial genome of Mentha spicata L. reveals multiple chromosomal configurations and RNA editing events

Mentha spicata L. is a valuable plant that yields spearmint oil, widely utilized in the pharmaceutical, chemical, and cosmetic industries. The mitochondrial genome (mitogenome) is an essential material for molecular breeding and evolution studies. Here, the mitogenome of M. spicata was assembled by combining Nanopore and Illumina reads. It consisted of a linear chromosome (Ch1) and two circular chromosomes (Ch2 and Ch3). Furthermore, we showed two pairs of repeats (R1 and R2) mediated recombinations resulting in multiple chromosomal configurations. The R1-mediated-recombination generated a large molecule formed by joining Ch2 and Ch1. Similarly, the R2-mediated-recombination generated a large molecule formed by joining Ch3 and Ch1. Then, we identified 17 mitochondrial plastid DNAs (MTPTs) by comparing the mitogenome and cpgenome. The MTPT14 was conserved in multiple species, which has undergone the same evolutionary process as the two organellar genomes among M. spicata, Hesperelaea palmeri and Castilleja paramensis. Based on the RNA-seq reads, 246 RNA editing sites were predicted, resulting in the conversion of cytosine to uracil bases. Furthermore, we successfully validated 40 out of 43 predicted sites. This project reported a complex structure of the M. spicata mitogenome resulting from repeat-mediated recombinations, which will provide valuable information for gene function study and the breeding of different varieties.

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

BackgroundThe chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation.ResultsAnalysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes.ConclusionThis study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

Plastid genome of Passiflora tripartita var. mollissima (poro-poro) from Huánuco, Peru

Passiflora tripartita var. mollissima, known locally as poro-poro, is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, only a few genetic data are available, which limits exploring its genetic diversity and developing new genetic studies for its improvement. We report the poro-poro plastid genome to expand the knowledge of its molecular markers, evolutionary studies, molecular pathways, and conservation genetics. Total genomic DNA was extracted from fresh leaves (herbarium voucher: USM:MHN331530). The DNA was sequenced using Illumina Novaseq 6000 platform providing 163,451 bp in length, with a large single-copy region of 85,525 bp and a small single-copy region of 13,518 bp, separated by a pair of inverted repeat regions (IR) of 32,204 bp, and the overall GC content was 36.87%. The chloroplast genome contains 129 genes (112 genes were unique and 17 genes were found duplicated in each IR region), including 85 protein-coding genes, 37 transfer RNA-coding genes, seven ribosomal RNA-coding genes, and 14 genes with introns (12 genes with one intron and two genes with two introns). The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis demonstrates poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study provides the basis for developing new molecular markers that constitutes a valuable resource for studying molecular evolution and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.

Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes

BackgroundPinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species.ResultsGenerally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification.ConclusionWe compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.

Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume.

Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.

Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Chloroplasts (cp) are important organelles in plant cells that have been widely used in phylogenetic, molecular evolution, and gene expression studies due to their conserved molecular structure. In this study, we obtained the complete cp genome of Trivalvaria costata (Annonaceae) and analyzed its structural characteristics. Additionally, we analyzed the rps12 gene in the phylogenetic framework of magnoliids. The T. costata cp genome comprises 162,002 bp and contains 132 genes. We detected 48 simple sequence repeats (SSRs) and identified 29 high-frequency codons as well as 8 optimal codons. Our multiple analyses show that codon usage bias is mainly influenced by natural selection. For the first time, we found the rps12 gene to be entirely located in the IR region (in Annona). In groups with exon 1 located in the single-copy (SC) region and exons 2–3 located in the inverted repeat (IR) region, the transition rate and synonymous substitution rate of exon 1 were higher than those of exons 2–3. Adaptive evolution identified a positive selection site (116) located in the 310-helix region, suggesting that the rps12 gene may undergo adaptive changes during the evolutionary history of magnoliids. This study enhances our knowledge regarding genetic information on T. costata and provides support for reduced substitution rates in the IR region.

Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae).

Cotinus is an oligo-specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa of Cotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships of Cotinus based on whole cp genomes, protein-coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113-114 genes were identified in the genomes. Seven non-coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genes matK and rps8 in the Cotinus cp genomes. Phylogenetic results confirmed that Cotinus is a monophyletic group but the widely distributed species Cotinus coggygria is not monophyletic. The divergence-time analysis suggested that Cotinus underwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny of Cotinus and related taxa.

Two Complete Mitochondrial Genomes of Leptobrachium (Anura: Megophryidae: Leptobrachiinae): Characteristics, Population Divergences, and Phylogenetic Implications.

The mustache toads Leptobrachium boringii and Leptobrachium liui are two attractive species in Megophryidae, in which adult males have mustache-like keratinized nuptial spines on their upper lip. However, both are under threat due to multiple factors, of which scientific studies are still very limited. In this study, two new complete mitochondrial genomes of L. boringii and L. liui were sequenced, assembled, and annotated based on next-generation sequencing. The mitogenome lengths of L. boringii and L. liui were found to be 17,100 and 17,501 bp, respectively, with both containing 13 protein coding genes, 23 tRNAs, 2 rRNAs, and 1 non-coding control region. Nucleotide diversity analyses indicate that atp8, atp6, and nad2 showed higher nucleotide diversity than cox1, cox3, and cytb. The intraspecific genetic distances among three different populations of L. boringii exceed 4%, and those between two populations of L. liui reach 7%. Phylogenetic relationships support their division into two subfamilies of Megophryidae (Leptobrachiinae and Megophryinae) as well as two species groups within Leptobrachium, corresponding to the number of keratinized nuptial spines (10-48 in the L. boringii species group vs. 2-6 in the L. liui species group). The two new mitogenomes reported in this study provide valuable data for future molecular evolutionary and conservation studies of the genus Leptobrachium and other Megophryidae toads.

The perspective of fish venom: An overview of the physiology, evolution, molecular and genetics

Fish venom has several biological activities, including enzyme activity, cytotoxicity, neurotoxicity, muscular toxicity, haemolytic, and cardiotoxicity, when they enter other species or a human being, they disrupt the physiological systems. Transcriptomic analysis of the fish venom glands revealed a large number of proteins relevant to the pharmacological activity even though they are not well-studied. The limitations in studying fish venoms also have an impact on their molecular characterization. This is partly because of the nature of fish venoms, as they are extremely unstable at normal ambient temperatures making them difficult to study. Venomous fish inhabit both marine and freshwater environments, they have specialized venom-delivery apparatuses. Venom delivery systems have evolved in a various animal species, originally for different purposes including defense, competition, as well as predation. In coastal areas, fish stings are a major problem because they have a serious toxic effect on fishermen, local communities, and visitors. In this study, we have discussed the general perspective of fish venom from marine and freshwater species in different aspects basically in their molecular evolution, physiology, diversity, transcriptome, and proteomic studies. We expect that this paper will provide readers with a unique perspective on understanding the current status of fish venom research as well as working for future studies. Therefore, the gap of knowledge acquired from this study will play as a baseline for researchers discovering new studies and using fish venom in a broader range of biomedical applications, and their biological information that can be used to develop drugs for pharmaceutical uses.

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organizations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organizations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal gene order reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and interchromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.

Complete mitochondrial genome of Rectorisluxiensis (Teleostei, Cyprinidae): characterisation and phylogenetic implications.

Mitochondrial genomes (mitogenomes) are widely used in scientific studies on phylogenetic relationships, molecular evolution and population genetics. Here, we sequenced and analysed the mitogenome of Rectorisluxiensis, a Yangtze River drainage endemic, but threatened cyprinid fish of Labeoninae. The complete mitogenome of R.luxiensis was 16,592 bp in length, encoding 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region. The mitogenome showed a high A+T content (58.2%) and a positive AT-skew (0.10) and negative GC-skew (-0.25) base composition pattern. All the 13 PCGs were found to start with ATG codons, except for the COXI, in which GTG was the start codon. The ratio of non-synonymous and synonymous substitutions (Ka/Ks) of all the 13 PCGs were less than 1, indicating negative or purifying selection evolved in these genes. Comparatively speaking, the evolutionary rate of ATP8 was the fastest and ND4L was the slowest. All tRNAs could fold into a typical cloverleaf secondary structure, except tRNASer1 that lacked a dihydrouridine arm. Phylogenetic relationships, based on the PCGs dataset of 91 mitogenomes of Labeoninae, showed that R.luxiensis grouped with Rectorisposehensis and they formed a monophyletic Rectoris. However, many non-monophyletic genera were revealed in labeoninae fishes, such as Cirrhinus, Decorus, Garra, Labeo and Pseudocrossocheilus, which indicated that the validities of some traditional genera required a further check. This study reported the complete mitogenome of R.luxiensis for the first time, which provided valuable data for future molecular evolution and conservation related studies of Rectoris and other species in Labeoninae.

A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei).

The golden mussel (Limnoperna fortunei) is a highly invasive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. In this study, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using PacBio HiFi, 10X, and Hi-C sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. A total of 34,862 protein-coding genes were predicted, of which 84.7% were functionally annotated. A significant (6.48%) proportion of the genome was found to be in a hemizygous state. Using the new genome, we have performed a genome-wide characterization of the Doublesex and Mab-3 related transcription factor gene family, which has been proposed as a target for population control strategies in other species. From the applied research perspective, a higher-quality genome will support genome editing with the aim of developing biotechnology-based solutions to control invasion. From the basic research perspective, the new genome is a high-quality reference for molecular evolutionary studies of Mytilida and other Lophotrochozoa, and it may be used as a reference for future resequencing studies to assess genomic variation among different golden mussel populations, unveiling potential routes of dispersion and helping to establish better control policies.

Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla.

RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade. Unexpectedly, RNase9 experienced an evolutionary scenario of "birth and death" in Ruminantia, and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues (epididymis, vas deferens or prostate). This expression pattern combined with the estimate that these genes duplicated during the middle Eocene, a time when Ruminantia become a successful lineage, suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this period. In contrast, all RNase9 genes were lost in the Cetacean lineage, which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean resources. This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla, providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP).

Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and deletion (indel) events, but available approaches exhibit limitations. To address these limitations, we developed Graphical Representation of Ancestral Sequence Predictions (GRASP), which efficiently implements maximum likelihood methods to enable the inference of ancestors of families with more than 10,000 members. GRASP implements partial order graphs (POGs) to represent and infer insertion and deletion events across ancestors, enabling the identification of building blocks for protein engineering. To validate the capacity to engineer novel proteins from realistic data, we predicted ancestor sequences across three distinct enzyme families: glucose-methanol-choline (GMC) oxidoreductases, cytochromes P450, and dihydroxy/sugar acid dehydratases (DHAD). All tested ancestors demonstrated enzymatic activity. Our study demonstrates the ability of GRASP (1) to support large data sets over 10,000 sequences and (2) to employ insertions and deletions to identify building blocks for engineering biologically active ancestors, by exploring variation over evolutionary time.

Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

BackgroundSexual stage surface antigens are potential targets of transmission-blocking vaccines (TBVs). The gametocyte and gamete surface antigen P230, a leading TBV candidate, is critical for red blood cell binding during exflagellation and subsequent oocyst development. Here, the genetic diversity of Pvs230 was studied in Plasmodium vivax parasite isolates from the China–Myanmar border (CMB) and central Myanmar.MethodsPlasmodium vivax isolates were collected in clinics from malaria-endemic areas of the CMB (143 samples) and Myanmar (23 samples). The interspecies variable part (IVP, nucleotides 1–807) and interspecies conserved part (ICP, 808–2862) of Pvs230 were amplified by PCR and sequenced. Molecular evolution studies were conducted to evaluate the genetic diversity, signature of selection, population differentiation, haplotype network, and population structure of the study parasite populations and publicly available Pvs230 sequences from six global P. vivax populations.ResultsLimited genetic diversity was observed for the CMB (π = 0.002) and Myanmar (π = 0.001) isolates. Most amino acid substitutions were located in the IVP and cysteine-rich domain of Pvs230. Evidence of positive selection was observed for IVP and purifying selection for ICP. Codon-based tests identified specific codons under natural selection in both IVP and ICP. The fixation index (FST) showed low genetic differentiation between East and Southeast Asian populations, with FST ranging from 0.018 to 0.119. The highest FST value (FST = 0.503) was detected between the Turkey and Papua New Guinea populations. A total of 92 haplotypes were identified in global isolates, with the major haplotypes 2 and 9 being the most abundant and circulating in East and Southeast Asia populations. Several detected non-synonymous substitutions were mapped in the predicted structure and B-cell epitopes of Pvs230.ConclusionsWe detected low levels of genetic diversity of Pvs230 in global P. vivax populations. Geographically specific haplotypes were identified for Pvs230. Some mutations are located within a potential B-cell epitope region and need to be considered in future TBV designs.Graphical

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in 1 or more species-a phenomenon observed among several important families of genes such as transporters and transcription factors-are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across 7 eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole-genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.

RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors.

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.

Biological challenges to conclusions from molecular phylogenies: behaviour strongly favours orb web monophyly, contradicting molecular analyses

Abstract This first-ever extensive review of the construction behaviour of orb webs, of webs secondarily derived from orbs, and of non-orbs shows that the evidence favouring monophyly over convergent evolution of orbs is stronger than previously appreciated. The two major orb-weaving groups, Uloboridae and Araneoidea, share 31 construction behaviour traits, 20 of which are likely to be both derived and to have feasible alternatives, making convergence an unlikely explanation. Convergence in two lineages seems unlikely, and convergence in five different lineages, as proposed in some recent molecular studies of phylogeny, is even less credible. A further set of seven shared responses in orb design to experimentally constrained spaces also supports orb monophyly. Finally, a ‘control’ case of confirmed convergence on similar ‘pseudo-orbs’ in a taxonomically distant group also supports this argument, as it shows a low frequency of behavioural similarities. I argue that the omission of behavioural data from recent molecular studies of orb web evolution represents a failure of the analytic techniques, not the data, and increases the risk of making mistakes. In general, phylogenetic studies that aim to understand the evolution of particular phenotypes can benefit from including careful study of the phenotypes themselves.