Low Sequence Divergence Research Articles

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.

Graphormer supervised de novo protein design method and function validation.

Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2-C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.

Detection of Felis catus Gammaherpesvirus 1 in Domestic Cat Saliva: Prevalence, Risk Factors, and Attempted Virus Isolation.

Felis catus gammaherpesvirus 1 (FcaGHV1) infects domestic cats worldwide, yet it has not been successfully propagated in cell culture, and little is known about how it is shed and transmitted. To investigate the salivary shedding of FcaGHV1, we quantified FcaGHV1 DNA in feline saliva by qPCR. For FcaGHV1-positive saliva, we sequenced a portion of the viral glycoprotein B (gB) gene and attempted to isolate the infectious virus by passage in several felid and non-felid cell lines. We detected FcaGHV1 DNA in 45/227 (19.8%) saliva samples with variable viral DNA loads from less than 100 to greater than 3 million copies/mL (median 4884 copies/mL). Multiple saliva samples collected from an infected cat over a two-month period were consistently positive, indicating that chronic shedding can occur for at least two months. Cat age, sex, and health status were not associated with shedding prevalence or viral DNA load in saliva. Feral status was also not associated with shedding prevalence. However, feral cats had significantly higher FcaGHV1 DNA load than non-feral cats. Sequencing of FcaGHV1 gB showed low sequence diversity and >99.5% nucleotide identity to the worldwide consensus FcaGHV1 gB sequence. We did not detect virus replication during the passage of FcaGHV1-positive saliva in cell culture, as indicated by consistently negative qPCR on cell lysate and supernatant. To our knowledge, these data show for the first time that cats in Canada are infected with FcaGHV1. The data further suggest that shedding of FcaGHV1 in saliva is common, can occur chronically over an extended period of time, and may occur at higher levels in feral compared to non-feral cats.

Analyzing genetic diversity of chloroplast genomes in Liliales

AbstractLiliales is a monocotyledonous order and contains both photosynthetic and mycoheterotrophic species that distribute locally or worldwide. In this study, thegenetic diversity of chloroplast genomes in Liliales was explored regarding theirnucleotide diversity and repeated composition. The analysis of nucleotide diversity revealed various hotspots in large and small single-copy regions whereas the IR regions had low sequence divergence. Although each family has specific hotspots, the rps15-ycf1 region was commonly found as a highly variable area in the cpDNA of observed taxa. In the cpDNA of Liliales, mononucleotide simple sequence repeat (SSR) is the most common type. The majority of SSRs are located in non-coding regions. Similarly, more long repeats were found in non-coding areas than in coding sequences. Additionally, the complement repeat exceeds forward type in the cpDNA of Liliales. The highest number of long repeats was found in Corsia dispar whereas that of SSRswas detected in Smilax china. The results of nucleotide diversity and repeat analyses provided fundamental information for further studies on population genetics, molecular marker development and evolutionary history of Liliales.® 2022 Journal of Science and Technology - NTTU

Datamining approaches for examining the low prevalence of N-acetylglutamate synthase deficiency and understanding transcriptional regulation of urea cycle genes.

Ammonia, which is toxic to the brain, is converted into non-toxic urea, through a pathway of six enzymatically catalyzed steps known as the urea cycle. In this pathway, N-acetylglutamate synthase (NAGS, EC 2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetyl coenzyme A. NAGS deficiency (NAGSD) is the rarest of the urea cycle disorders, yet is unique in that ureagenesis can be restored with the drug N-carbamylglutamate (NCG). We investigated whether the rarity of NAGSD could be due to low sequence variation in the NAGS genomic region, high NAGS tolerance for amino acid replacements, and alternative sources of NAG and NCG in the body. We also evaluated whether the small genomic footprint of the NAGS catalytic domain might play a role. The small number of patients diagnosed with NAGSD could result from the absence of specific disease biomarkers and/or short NAGS catalytic domain. We screened for sequence variants in NAGS regulatory regions in patients suspected of having NAGSD and found a novel NAGS regulatory element in the first intron of the NAGS gene. We applied the same datamining approach to identify regulatory elements in the remaining urea cycle genes. In addition to the known promoters and enhancers of each gene, we identified several novel regulatory elements in their upstream regions and first introns. The identification of cis-regulatory elements of urea cycle genes and their associated transcription factors holds promise for uncovering shared mechanisms governing urea cycle gene expression and potentially leading to new treatments for urea cycle disorders.

Influence of the Rate of Changes in the COX1 Gene on Body Size and Sexual Selection in Carp Hybridization

The influence of mtDNA cytochrome c-oxidase I gene fragment variability on body length was studied in twelve species of cyprinids, which may have hybrids with Rutilus rutilus L. and Abramis brama L., and in reciprocal hybrids (RA, AR) and alloplasmatic backcrosses (ARR, RAA) of roach (R) and bream (A). It has been established that the rate of nucleotide substitutions in COX1 is negatively related not only to body size but also to fish life span, which differentiates them into two groups: group I – species with a high rate of COX1 changes and a relatively small body size and group II – species with low sequence variability and relatively large body size. The boundary for the distinguished groups runs between species the same genus Leuciscus leuciscus and L. idus: with a twofold decrease in the rate of substitutions in ide, a twofold increase in body size and lifespan occurs, which indicates a decrease in the rate of cellular respiration and free radical leak, and the exact mitonuclear match respiratory complexes. Presumably, the decrease in the rate of COX1 changes in species of group II and in bleak Alburnus alburnus is associated with an increase in the size of genome, which provides additional protection of genes from chemical mutagens and, regardless of body size, reduces the rate of aerobic metabolism. It has been experimentally shown that mtDNA affects body length. When bream mtDNA is included in the roach nuclear genome, ARR backcrosses have the body length of a bream and high viability, while RAA backcrosses with roach mtDNA and the bream nuclear genome inherit the roach body length and reduce viability. Species of group II are not able to effectively use the highly polymorphic mtDNA of species of group I, which is also manifested by a violation of the inheritance of a longer bream body length in RA hybrids and leads to reproductive isolation. Group I species, such as Rutilus rutilus, can include mtDNA of both groups in their genome, which underlies sexual selection in hybridization. Accordingly, sexual size dimorphism has a genetic origin, and body size for a potential partner can be a signal for determining the mitonuclear compatibility of genomes in respiratory complexes.

Phylogenetic and biogeographic history of brook lampreys (Lampetra: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data.

The Adriatic brook lamprey, Lampetra zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy. Lampetra from the Neretva River system in Croatia and Bosnia and Herzegovina and the Morača River system in Montenegro that were previously identified as L. zanandreai were recently described as a new species Lampetra soljani Tutman, Freyhof, Dulčić, Glamuzina & Geiger 2017 based on morphological data and a genetic distance between the two species of roughly 2.5% in the DNA barcoding gene cytochrome oxidase I (COI). Since DNA barcodes for L. zanandreai are only available for one population from the upper Po River in northwestern Italy, we generated additional COI nucleotide sequence data of this species from Switzerland, northeastern and central Italy comprising near topotypic material and obtained GenBank sequences of the species from Slovenia to better assess the evolutionary history of the two brook lamprey species in the river basins of the Adriatic Sea. Our data show a low sequence divergence of <1% between L. zanandreai from Switzerland, northeastern and central Italy and Slovenia and the Balkan species L. soljani. However, members of the population previously identified as 'L. zanandreai' from northwest Italy are genetically highly divergent from those of L. zanandreai and likely belong to an undescribed species, L. sp. 'upper Po'. The presence of a unique and highly divergent brook lamprey lineage in the upper Po River suggests that L. zanandreai and Lampetra sp. 'upper Po' may have evolved in separate paleo drainages during the formation of the modern Po Valley subsequent to marine inundations in the Pliocene.

A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon Acipenser fulvescens Displaying Epithelial Skin Lesions.

Herpesvirus infections of sturgeon pose a potential threat to sturgeon culture efforts worldwide. A new epitheliotropic herpesvirus named Acipenser herpesvirus 3 (AciHV-3) was detected in hatchery-reared Lake Sturgeon Acipenser fulvescens displaying skin lesions in central Canada. The growths were discovered in the fall, reached average prevalence levels of 0.2-40% and eventually regressed. No unusual mortality was observed. The cellular changes within the lesions included epithelial hyperplasia and were reminiscent of other herpesvirus infections. The virus was not evident in lesions examined by electron microscopy. Skin tissue homogenates from symptomatic sturgeon produced atypical cytopathic effects on a primary Lake Sturgeon cell line, and next-generation sequence analysis of the DNA samples revealed the presence of an alloherpesvirus. A new genotyping PCR assay targeting the major capsid protein sequence detected AciHV-3 in symptomatic Lake Sturgeon as well as other apparently healthy sturgeon species. Bayesian inference of phylogeny reconstructed with a concatenation of five alloherpesvirus core proteins revealed a new Alloherpesviridae lineage isomorphic with a new genus. The presence of AciHV-3 homologs in cell lines and sturgeon sequence datasets, low sequence divergence among these homologs and branching patterns within the genotyping phylogeny provide preliminary evidence of an endogenous virus lifestyle established in an ancestral sturgeon.

Effect of Different Types of Sequence Data on Palaeognath Phylogeny.

Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements, introns, and ultraconserved elements. Using the noncoding loci together with protein-coding loci, this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene tree-based approaches supported rheas as the group that diverged first among groups (1)-(4). Whereas gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than noncoding loci. Regarding the relationships of (1)-(4), the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogeneous model and suggested the clustering of kiwi and cassowaries and emu the most likely with ∼40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.

General Strategies for RNA X-ray Crystallography.

An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA-protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; (2) difficulty creating crystal contacts due to low sequence diversity; and (3) limited methods for phasing. Various approaches have been developed to address these obstacles, such as native RNA purification, engineered crystallization modules, and incorporation of proteins to assist in phasing. In this review, we will discuss these strategies and provide examples of how they are used in practice.

Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen.

The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

Varying strength of selection contributes to the intragenomic diversity of rRNA genes

Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.

Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza.

The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.

Assessing Morphological Species and Interspecific Relationships in North American Grapeferns (Sceptridium; Ophioglossaceae) Using ISSR Markers

Abstract— Relationships among North American Sceptridium (sensu Škoda) species are often difficult to assess because of few stable distinguishing characters and high intraspecific variability. We used ISSR-PCR to examine relationships among four samples of Holubiella, 24 samples representing four diploid North American Sceptridium species, and a Russian Sceptridium sample. Nine ISSR primers yielded 147 polymorphic loci. We generated three neighbor-joining dendrograms using a Jaccard, Nei &amp; Li, or Dice coefficient. All three coefficients cluster based solely on the presence of bands and not the absence. ISSR data analyses across all three coefficients were consistent with published analyses of DNA sequence data in supporting Holubiella as sister to all Sceptridium species sampled. Sister group relationships among the four Sceptridium species were not consistent across all three neighbor-joining analyses, and bootstrap support was generally low. However, 26 of the 29 samples consistently clustered with other samples of similar morphology, and these clusters generally supported current species concepts. In taxa such as Sceptridium, with low DNA sequence variability among species, ISSR-PCR may provide an important tool for evaluating morphologically defined species, but additional data are necessary for establishing robust hypotheses of phylogenetic relationships.

Isolation, typing, and drug susceptibility of Leishmania (Leishmania) infantum isolates from dogs of the municipality of Embu das Artes, an endemic region for canine leishmaniasis in Brazil.

The parasitic protozoa Leishmania (Leishmania) infantum is the etiological agent of human visceral leishmaniasis and canine leishmaniasis in South America, where Brazil is the most affected country. This zoonotic disease is transmitted by the bite of an infected phlebotomine sand fly and dogs constitute the main domestic reservoir of the parasite. In this study, we screened 2348 dogs of the municipality of Embu das Artes, Brazil, for antibodies against the parasite. Prevalence for canine leishmaniasis seropositivity was 2.81%, as assessed using a Dual-Path Platform rapid test for canine leishmaniasis. Twenty-five seropositive dogs were euthanized for parasite isolation and 14 isolates were successful obtained. Nucleotide sequencing of the internal transcribed spacer confirmed the isolates to be L. (L.) infantum, and very low sequence variability was observed among them. The in vitro susceptibility to miltefosine and paromomycin was assessed and moderate variation in paromomycin susceptibility was found among the isolates in the promastigote and intracellular amastigote stages. On the other hand, in vitro susceptibility to miltefosine of these isolates was homogenous, particularly in the amastigote stage (EC50 values from 0.69 to 2.07μM). In addition, the miltefosine sensitivity locus was deleted in all the isolates, which does not corroborate the hypothesis that the absence of this locus is correlated with a low in vitro susceptibility. Our findings confirm that the municipality of Embu das Artes is endemic for canine leishmaniasis and that isolates from this region are susceptible to paromomycin and miltefosine, indicating the potential of these drugs to be clinically evaluated in the treatment of human visceral leishmaniasis in Brazil.

Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns.

Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.

Analyzing genetic diversity of chloroplast genomes in Liliales

AbstractLiliales is a monocotyledonous order and contains both photosynthetic and mycoheterotrophic species that distribute locally or worldwide. In this study, thegenetic diversity of chloroplast genomes in Liliales was explored regarding theirnucleotide diversity and repeated composition. The analysis of nucleotide diversity revealed various hotspots in large and small single-copy regions whereas the IR regions had low sequence divergence. Although each family has specific hotspots, the rps15-ycf1 region was commonly found as a highly variable area in the cpDNA of observed taxa. In the cpDNA of Liliales, mononucleotide simple sequence repeat (SSR) is the most common type. The majority of SSRs are located in non-coding regions. Similarly, more long repeats were found in non-coding areas than in coding sequences. Additionally, the complement repeat exceeds forward type in the cpDNA of Liliales. The highest number of long repeats was found in Corsia dispar whereas that of SSRswas detected in Smilax china. The results of nucleotide diversity and repeat analyses provided fundamental information for further studies on population genetics, molecular marker development and evolutionary history of Liliales.® 2022 Journal of Science and Technology - NTTU

Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species

BackgroundThe large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species.ResultsThe complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus.ConclusionThe chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences

Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, numerous new sequences, even in organisms other than mosquitos, have been identified and characterized.In this study, we analyzed nucleotide and protein sequences of mesoniviruses with a wide range of molecular tools including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping and phylodynamic reconstruction. We also sought to revaluate new mesoniviruses sequence positions within the family, proposing a taxonomic revision.The different sub-lineages of mosquito mesoniviruses sequences presented low sequence diversity and entropy, with incongruences to the existing taxonomy being found after an extensive phylogenetic characterization. High sequence discrepancy and differences in genome organization were found between mosquito mesoniviruses and other mesoniviruses, so their future classification, as other meso-like viruses that are found in other organisms, should be approached with caution.No evidence of frequent recombination was found, and mesonivirus genomes seem to evolve under strong purifying selection. Insufficient data by root-to-tip analysis did not yet allow for an adequate phylogeographic reconstruction.