Phylogenetic Classification Research Articles

ATP-Binding Cassette G Transporters and Their Multiple Roles Especially for Male Fertility in Arabidopsis, Rice and Maize.

ATP-binding cassette subfamily G (ABCG) transporters are extensive in plants and play essential roles in various processes influencing plant fitness, but the research progress varies greatly among Arabidopsis, rice and maize. In this review, we present a consolidated nomenclature and characterization of the whole 51 ABCG transporters in maize, perform a phylogenetic analysis and classification of the ABCG subfamily members in maize, and summarize the latest research advances in ABCG transporters for these three plant species. ABCG transporters are involved in diverse processes in Arabidopsis and rice, such as anther and pollen development, vegetative and female organ development, abiotic and biotic stress response, and phytohormone transport, which provide useful clues for the functional investigation of ABCG transporters in maize. Finally, we discuss the current challenges and future perspectives for the identification and mechanism analysis of substrates for plant ABCG transporters. This review provides a basic framework for functional research and the potential application of ABCG transporters in multiple plants, including maize.

Genetic diversity and bioinformatic analysis of the HPV-45 L1 gene in Iranian women with normal cytology

BackgroundHuman papillomavirus type 45 is a potential risk of 3-9% of cervical cancers in a geographic-dependent pattern but it is uncommon in women with normal cytology. MethodsIn this study, we aimed to investigate the HPV-45 L1 gene to find the predominant variants in women with normal cytology, as a general population. We analyzed the nucleotide and amino acid changes along the L1 gene for embedding in N-glycosylated sites, external surface loops, and for positive/negative selection. ResultsThe B1 sub-lineage was the most frequent variants (40%), followed by each of B2, A1, and A2, accounting for 20%. None of missense variations affected the HPV-45 L1 function or located in the N-glycosylated sites. Three amino acid deletions occurred in the C-terminus and seven codons were under negative selection. Also, four mutations were embedded in the surface loops; N81S in BC loop, I166V in DE loop, and S383G/N and Q392H both in HI loop. ConclusionGiven the importance of HPV-45 and its sub-lineages in developing cervical cancer, a phylogenetic classification of HPV-45 circulating in general population may assist in setting the screening programs, diagnosis methods, and future epidemiological studies.

Highly Virulent and Multidrug-Resistant Escherichia coli Sequence Type 58 from a Sausage in Germany.

Studies have previously described the occurrence of multidrug-resistant (MDR) Escherichia coli in human and veterinary medical settings, livestock, and, to a lesser extent, in the environment and food. While they mostly analyzed foodborne E. coli regarding phenotypic and sometimes genotypic antibiotic resistance and basic phylogenetic classification, we have limited understanding of the in vitro and in vivo virulence characteristics and global phylogenetic contexts of these bacteria. Here, we investigated in-depth an E. coli strain (PBIO3502) isolated from a pork sausage in Germany in 2021. Whole-genome sequence analysis revealed sequence type (ST)58, which has an internationally emerging high-risk clonal lineage. In addition to its MDR phenotype that mostly matched the genotype, PBIO3502 demonstrated pronounced virulence features, including in vitro biofilm formation, siderophore secretion, serum resilience, and in vivo mortality in Galleria mellonella larvae. Along with the genomic analysis indicating close phylogenetic relatedness of our strain with publicly available, clinically relevant representatives of the same ST, these results suggest the zoonotic and pathogenic character of PBIO3502 with the potential to cause infection in humans and animals. Additionally, our study highlights the necessity of the One Health approach while integrating human, animal, and environmental health, as well as the role of meat products and food chains in the putative transmission of MDR pathogens.

An investigation of Miconia tetrandra (Melastomataceae: Miconieae): Phylogenetic placement and taxonomy

Miconia tetrandra, a morphologically distinctive species restricted to the Caribbean region, is provided with an updated assessment of its phylogenetic position and taxonomy. A detailed description and nomenclatural treatment are provided, along with a consideration of phenology, distribution and habitat, and citation of specimens examined. The species is a member of the Caribbean clade, and it is unusual within Miconia in having flowers with only four stamens (alternating with the petals), with short, obovate, yellow anthers that each open by two large pores. Miconia tetrandra is morphologically quite divergent from, but is likely related to, a clade comprised by M. angustifolia, M. urbanii, and M. biflora, and these three species traditionally have been included within the genus Tetrazygia. In contrast, M. tetrandra usually has been placed within Miconia.

Contrasting Responses of the Microbial Community Structure and Functional Traits to Soil pH in Purple Soils

To clarify the effect of pH on the structure and functional traits of soil microbial communities in purple soils, three purple upland soils developed from the same parent material that differed in pH were selected as the research objects, and metagenomic shotgun sequencing was used to investigate the structure and functional traits of the microbial communities among different pH soils. The shotgun sequencing identified a total of 89 phyla, 222 classes, 527 orders, 1009 families, 2769 genera, and 14354 species in these soils. Regardless of the phylogenetic classification level, the microbial community structures of these three purple soils with different pHs were significantly different. RDA results corroborated the highly significant difference in the microbial community structures among the three purple soils with different pHs, and the soil properties tested here all had significant correlations with soil microbial community structure, in which the soil pH had the greatest effect (R2=0.9985, P=0.001). However, the results of investigating the microbial community functions revealed that the main metabolic processes of the three purple soils were all involved in unknown functions, global and overview maps, amino acid metabolism, carbohydrate metabolism, ammonia assimilation, etc. There was almost no significant difference in the relative abundance of microbes in the three purple soils annotated with the same function regardless of the COG/KEGG functional database and nitrogen cycling functional database, indicating that the overall function trait of soil microbial community was relatively conservative and not easily affected by environmental factors.

Phylogenetic Classification and Functional Review of Autotransporters.

Autotransporters are the core component of a molecular nano-machine that delivers cargo proteins across the outer membrane of Gram-negative bacteria. Part of the type V secretion system, this large family of proteins play a central role in controlling bacterial interactions with their environment by promoting adhesion to surfaces, biofilm formation, host colonization and invasion as well as cytotoxicity and immunomodulation. As such, autotransporters are key facilitators of fitness and pathogenesis and enable co-operation or competition with other bacteria. Recent years have witnessed a dramatic increase in the number of autotransporter sequences reported and a steady rise in functional studies, which further link these proteins to multiple virulence phenotypes. In this review we provide an overview of our current knowledge on classical autotransporter proteins, the archetype of this protein superfamily. We also carry out a phylogenetic analysis of their functional domains and present a new classification system for this exquisitely diverse group of bacterial proteins. The sixteen phylogenetic divisions identified establish sensible relationships between well characterized autotransporters and inform structural and functional predictions of uncharacterized proteins, which may guide future research aimed at addressing multiple unanswered aspects in this group of therapeutically important bacterial factors.

Let there be clades: phylogenetics ofMimosaseriesPachycarpaeandSetosae(Fabaceae) improves the infrageneric classification of the genus

AbstractFull implementation of phylogenetic classifications remains pending, particularly to delimit infrageneric divisions of large genera. Mimosa, one of the largest genera of Fabaceae, includes five sections and 41 series, most of which are not monophyletic. Here we investigated the phylogenetic relationship among species of Mimosa series Pachycarpae and Setosae, two diverse series from the Brazilian Cerrado (savanna) Domain. We analysed morphological and molecular data for a wide taxonomic sample in a total-evidence approach. Our results show the non-monophyly of these series is more problematic than previously realized and extends to M. series Piresianae. Nonetheless, most taxa of M. series Pachycarpae and Setosae fall in a clade, which has an enlarged underground organ as one of its synapomorphies and an important functional trait underlying adaptation to fire in the Cerrado Domain. On the basis of these results, and after transferring some species to M. series Piresianae, we synonymize M. series Setosae under M. series Pachycarpae. These updates are a first step towards aligning the infrageneric classification of Mimosa with the tenets of phylogenetic systematics.

Retrospective Detection and Complete Genomic Sequencing of Canine morbillivirus in Eurasian Otter (Lutra lutra) Using Nanopore Technology.

The Eurasian otter (Lutra lutra) is a piscivorous apex predator in aquatic habitats, and a flagship species of conservation biology throughout Europe. Despite the wide distribution and ecological relevance of the species, there is a considerable lack of knowledge regarding its virological and veterinary health context, especially in Central Europe. Canine morbillivirus (Canine distemper virus (CDV)) is a highly contagious viral agent of the family Paramyxoviridae with high epizootic potential and veterinary health impact. CDV is present worldwide among a wide range of animals; wild carnivores are at particular risk. As part of a retrospective study, lung-tissue samples (n = 339) from Eurasian otters were collected between 2000 and 2021 throughout Hungary. The samples were screened for CDV using a real-time RT-PCR method. Two specimens proved positive for CDV RNA. In one sample, the complete viral genome was sequenced using a novel, pan-genotype CDV-specific amplicon-based sequencing method with Oxford Nanopore sequencing technology. Both viral sequences were grouped to a European lineage based on the hemagglutinin-gene phylogenetic classification. In this article, we present the feasibility of road-killed animal samples for understanding the long-term dynamics of CDV among wildlife and provide novel virological sequence data to better understand CDV circulation and evolution.

Genome-wide identification and expression analysis of the NAC transcription factor family in Saccharum spontaneum under different stresses

ABSTRACT The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The NAC family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the NAC gene family in the wild species Saccharum spontaneum has not been systematically studied. In this study, 115 SsNAC genes were identified in the S. spontaneum genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the SsNAC family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The SsNAC gene has different expression patterns at different developmental stages of stems and leaves. Further qRT–PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 SsNAC genes, indicating that these genes may play a key role in the resistance of S. spontaneum to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the NAC transcription factor family, providing a reference for further functional studies of the SsNAC gene.

Phylogenetic relationship among taxa in the genus Adonis L. collected from Türkiye based on nrDNA internal transcribed spacer (ITS) markers.

Genus Adonis L. contain approximately 40 annual and perennial species, which are widely distributed in the temperate zones of Asia and Europe, and less frequently in southwestern Asia, northern Africa and the Mediterranean region. The aim of the study was to evaluate the phylogenetic relationship among Adonis taxa collected from Türkiye based on nrDNA Internal transcribed spacer (ITS) markers. Samples of 64 individual genotypes from 21 populations of 10 Adonis taxa were collected from different regions of the country during vegetation period between 2014 and 2018. ITS1, ITS4, P16 and P25 primers within ITS technique was used to genotype the plant materials. Then, genotypic data was used to estimate magnitude and organization of infraspecific variation in different populations of Adonis. About 600bp DNA sequences were obtained from each 64 Adonis genotypes belonging to 21 different populations. The dendrogram obtained from Adonis taxa and out-group sequences had two large main groups. While the out-group species were placed in the first large main group, the sect. Consiligo (perennial) and sect. Adonis (annuals) were placed in different sub-groups of the second large main group. Genetic similarity among Adonis taxa varied between A. microcarpa and A. dentata (98.46%). Principal component analysis indicated that two important components in Adonis taxa genotypes. The expected heterozygosity ranged from 0.0252 (sub-population A) to 0.3460 (sub-population C), with an average of 0.1154. In addition, population differentiation measurements (Fst) ranged from 0.0025 (sub-population C) to 0.9016 (sub-population A) with a relatively high average 0.6601. Present analyses revealed that phylogenetic classification (grouping) of Adonis taxa largely depended on morphological structure and present ITS primers were quite efficient in putting forth the genetic diversity of such species. The results of this study suggested that ITS markers could be used in the identification of genetic diversity among the Adonis taxa. The results obtained from molecular data can be used to explore the genetic variation pattern, population structure, and the evolutionary history of genus Adonis in the future.

Intra-genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing.

SummaryRibosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large‐scale exploration of environmental microbial diversity through metabarcoding approaches has been focused mainly on the V4 and V9 regions of the 18S rRNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra‐genomic variability). Here we explored the intra‐genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra‐genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with <97% similarity. Of the different sequencing methods, Illumina showed the highest number of contaminations (i.e. environmental DNA, cross‐contamination, tag‐jumping), revealed by its high sequencing depth; and MinION showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results highlight the requirement for a careful interpretation of Illumina‐based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full‐length rDNA environmental metabarcoding surveys.

Conflicting signals in phylogenetic relationships and taxonomy of Anatolian endemic Silene sordida (Caryophyllaceae)

Silene sordida is a Southwest Anatolian endemic that shows highly contradicting signals regarding its actual classification. Using morphological, molecular, and palynological data we here investigate phylogeny and taxonomy of S. sordida. Morphological and palynological features of S. sordida are compared to the species known as very closely related to S. sordida. In addition, we generated DNA sequences of three nuclear and one plastid loci from S. sordida and some allied species belonging to several sections and analyzed these data together with the available sequence data of corresponding taxa. Our findings strongly support the unrelatedness of S. sordida with the section Atocion. The relationship between S. sordida and the section Cryptoneurae and S. odontopetala remains unstable among the four loci analyzed. Both morphological and molecular evidence suggest the recognition of a new monotypic section (here named “Sordidae”).

Polyphyly of the genus Stenurella (Coleoptera, Cerambycidae): Consensus of morphological and molecular data

Stenurella genus is represented by nine small-sized and widely distributed Palaearctic species. Representatives of the genus play a key role in the pollination of wild angiosperms, accelerate the detritus cycle and make a significant contribution to the forest food web. A number of species with heterogeneous morphological features found within the single Stenurella genus indicate the need for revision of the taxonomy this genus. The previous attempt to resolve the intrageneric composition of Stenurella was rather artificial because it did not take into an account evolutionary relationships. In this study we tested the existing model of Stenurella intrageneric subdivision using both morphological and molecular approaches. Our results showed that the genus Stenurella is polyphyletic and consists of two unrelated clades. The first clade comprises six species (S. jaegeri, S. novercalis, S. bifasciata, S. melanura, S. hybridula and S. approximans) and the second includes three species (S. septempunctata, S. vaucheri and S. nigra). Moreover, we found that the second clade is closely related to Rutpela due to both morphological and molecular phylogeny. Based on our findings, we revised the present structure of the genus Stenurella and transferred three species of the second clade to the genus Rutpela, sensu novo. The genus Rutpela was redescribed in the light of our results. Furthermore, we subdivided the genus Stenurella, sensu nov. into two subgenera, Stenurella, subgen. sensu nov. and Priscostenurella, subgen. sensu nov., respectively. Also, the genus Rutpela, sensu nov. was subdivided into four subgenera including Nigrostenurella, Rutpela, Eduardvivesia, subgen. nov. and Nigromacularia, subgen. nov. The assessment of the place of Stenurella, sensu novo and Rutpela, sensu novo within Lepturini based on molecular phylogeny, showed that Stenurella, sensu novo belongs to the Anoplodera-branch and Rutpela, sensu novo nested within the Leptura-branch. These together with morphological features confirmed our idea of the evolutionary distinctiveness of Stenurella, sensu novo and Rutpela, sensu novo. We assumed that the general external morphological similarity of Stenurella, sensu novo and Rutpela, sensu novo was the result of convergent evolution, driven by mimetic selection toward imitation of ants or wasps. Finally, our study establishes a natural phylogenetic taxonomy of Stenurella.

Cloning and functional characterization of three sesquiterpene synthase genes from Chamaecyparis formosensis Matsumura

Terpene synthase (TPS) analysis may contribute to a better understanding of terpenoids biosynthesis and the evolution of phylogenetic taxonomy. Chamaecyparis formosensis Matsumura is an endemic and valuable conifer of Taiwan. Its excellent wood quality, fragrance, and durability make it become the five precious conifers in Taiwan. In this study, three sesquiterpene synthase genes that belong to the TPS-d2 clade were isolated and characterized through in vitro reaction of recombinant protein and in vivo reaction of Escherichia coli heterologous expression system. The main product of Cf-GerA was germacrene A using GC/MS analysis, while the product of Cf-Aco and Cf-Gor were identified as acora-4(14),8-diene and (5R,6R,10S)-α-gorgonene by using NMR analysis. These are the first reported enzymes that biosynthesize acora-4(14),8-diene and (5 R,6 R,10 S)-α-gorgonene. Both sesquiterpene synthases may isomerize the farnesyl pyrophosphate substrate to nerolidyl pyrophosphate for further cyclization. Cf-Aco may catalyze 1,6-cyclization of nerolidyl cation while Cf-Gor may catalyze through an uncharged intermediate, isogermacrene A.

Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana.

Simple SummaryThe true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

A worldwide phylogenetic classification of the Poaceae (Gramineae) III: An update

AbstractWe present an updated worldwide phylogenetic classification of Poaceae with 11 783 species in 12 subfamilies, 7 supertribes, 54 tribes, 5 super subtribes, 109 subtribes, and 789 accepted genera. The subfamilies (in descending order based on the number of species) are Pooideae with 4126 species in 219 genera, 15 tribes, and 34 subtribes; Panicoideae with 3325 species in 242 genera, 14 tribes, and 24 subtribes; Bambusoideae with 1698 species in 136 genera, 3 tribes, and 19 subtribes; Chloridoideae with 1603 species in 121 genera, 5 tribes, and 30 subtribes; Aristidoideae with 367 species in three genera and one tribe; Danthonioideae with 292 species in 19 genera and 1 tribe; Micrairoideae with 192 species in nine genera and three tribes; Oryzoideae with 117 species in 19 genera, 4 tribes, and 2 subtribes; Arundinoideae with 36 species in 14 genera and 3 tribes; Pharoideae with 12 species in three genera and one tribe; Puelioideae with 11 species in two genera and two tribes; and the Anomochlooideae with four species in two genera and two tribes. Two new tribes and 22 new or resurrected subtribes are recognized. Forty‐five new (28) and resurrected (17) genera are accepted, and 24 previously accepted genera are placed in synonymy. We also provide an updated list of all accepted genera including common synonyms, genus authors, number of species in each accepted genus, and subfamily affiliation. We propose Locajonoa, a new name and rank with a new combination, L. coerulescens. The following seven new combinations are made in Lorenzochloa: L. bomanii, L. henrardiana, L. mucronata, L. obtusa, L. orurensis, L. rigidiseta, and L. venusta.

Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance.

Each year, seasonal influenza results in high mortality and morbidity. The current classification of circulating influenza viruses is mainly focused on the hemagglutinin gene. Whole-genome sequencing (WGS) enables tracking mutations across all influenza segments allowing a better understanding of the epidemiological effects of intra- and inter-seasonal evolutionary dynamics, and exploring potential associations between mutations across the viral genome and patient’s clinical data. In this study, mutations were identified in 253 Influenza A (H3N2) clinical isolates from the 2016-2017 influenza season in Belgium. As a proof of concept, available patient data were integrated with this genomic data, resulting in statistically significant associations that could be relevant to improve the vaccine and clinical management of infected patients. Several mutations were significantly associated with the sampling period. A new approach was proposed for exploring mutational effects in highly diverse Influenza A (H3N2) strains through considering the viral genetic background by using phylogenetic classification to stratify the samples. This resulted in several mutations that were significantly associated with patients suffering from renal insufficiency. This study demonstrates the usefulness of using WGS data for tracking mutations across the complete genome and linking these to patient data, and illustrates the importance of accounting for the viral genetic background in association studies. A limitation of this association study, especially when analyzing stratified groups, relates to the number of samples, especially in the context of national surveillance of small countries. Therefore, we investigated if international databases like GISAID may help to verify whether observed associations in the Belgium A (H3N2) samples, could be extrapolated to a global level. This work highlights the need to construct international databases with both information of viral genome sequences and patient data.

Multiplex polymerase chain reaction typing scheme based on Escherichia coli O157:H7 Sakai prophage (Sp)-associated genes

ObjectivesEscherichia coli strains of the O157 serogroup include significant foodborne pathogens: enterohemorrhagic E. coli (EHEC) and enteropathogenic E. coli, which are responsible for a considerable number of hospitalizations and deaths worldwide each year. There is a constant need for rapid, reliable, and easy-to-use methods for their identification, typing, and phylogenetic classification. In this study, we proposed a new multiplex polymerase chain reaction (PCR)–based typing system for pathogenic E. coli, focusing on the O157 serogroup. MethodsWe designed primers targeting 12 lambdoid prophage regions carried by the prototypic polylysogenic strain of EHEC, the O157:H7 Sakai strain. The reactions were tested in vitro as well as in silico with the PubMLST database. ResultsThe PCR assays can be grouped into four multiplex reactions, and their results can be given as a four-digit code. In vitro and in silico testing showed that these Sakai prophage regions are prevalent not only in E. coli O157 strains but also in Shiga toxigenic E. coli non-O157 strains and the method provides appropriate resolution. ConclusionsThe proposed method could be a valuable tool in epidemiologic tracing and preliminary phylogenetic grouping of this diverse group of pathogens.

The Retrospective on Atypical Brucella Species Leads to Novel Definitions.

The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.

Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda’s genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1–15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30–35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome’s repetitive fraction. The satellite DNA families’ repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.