Phylogenetic Classification Research Articles

Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

Background2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato.ResultsA total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity.ConclusionsOur study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

Genome Sequences and Phylogeny of Two Duck Hepatitis B Viruses.

Duck hepatitis B virus (DHBV) infection in Pekin ducks is a model for human hepatitis B. Sequence variations may contribute to host therapy responses against the virus. We provide full genome sequences of two DHBVs from France, their phylogenetic classification, and their sequence variability.

Taxonomic study of scallops (Pectinidae: mollusca, bivalvia) from Pliocene deposits (Almería, SE Spain)

A taxonomic study has been carried out on scallops (family Pectinidae: Mollusca, Bivalvia) occurring in the lower-earliest middle Pliocene deposits of the Campo de Dalías, Almería-Níjar Basin, and Carboneras Basin (province of Almería, SE Spain). The recently proposed suprageneric phylogenetic classification scheme for the family (Waller, 2006a) has been followed. Twenty two species in twelve genera (Aequipecten, Amusium, Chlamys, Flabellipecten, Flexopecten, Gigantopecten, Hinnites, Korobkovia, Manupecten, Palliolum, Pecten, and Pseudamussium) and three subfamilies (Chalmydinae, Palliolinae, and Pectininae) have been identified. This number of species is higher than previously reported for the same area. Additionally, the phylogenetic classification followed in this paper modifies the species attributions formerly used.

Palynology of selected species of Blechnaceae (Polypodiopsida: Polypodiales)

The Blechnaceae is a family of leptosporangiate ferns with a wide geographical distribution. Recent phylogenies revealed several lineages within the family, culminating in a classification system comprising 25 recognized genera grouped into three subfamilies. Spore surface morphology has major importance in the taxonomy of the group, but there is limited information on the relevance of other palynological characters. This study aimed to examine whether spore morphology aids in distinguishing genera of Blechnaceae according to the current phylogenetic classification. Spores from 28 species distributed in 12 genera of the subfamilies Blechnoideae, Stenochlaenoideae, and Woodwardioideae were examined. Specimens were acetolyzed, measured, described, and illustrated using light and scanning electron microscopy. The analyzed spores were medium to large in size, with a monolete scar of varied size, straight, and without margo. The perine was three-layered, except in the subfamily Stenochlaenoideae, which showed a single-layered perine. Blechnoideae was the most palynologically diverse subfamily. Woodwardioideae and Stenochlaenoideae spore characters had high diagnostic value for identification at the genus level. Austroblechnum and Blechnum showed high similarity; no single spore character could be used to discriminate between species of these genera. Blechnum anthracinum was the only species within its genus to exhibit cristate spores, with filaments and perforations. Morphometric analysis did not prove to be a useful tool for differentiating subfamilies or genera, possibly because of the influence of polyploid individuals. This investigation revealed unique spore characters for some genera and provided morphological descriptions that allow identification at the species level, contributing to the taxonomic study of Blechnaceae.

Transmission of pre-XDR and XDR-TB in the Mumbai Metropolitan Region, India

Background: Multidrug-resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis complex (MTBC) strains are a great challenge for tuberculosis (TB) control in India. Still, factors driving the MDR/XDR epidemic in India are not well defined. Methods: Whole genome sequencing (WGS) data from 1 852 MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai were used for phylogenetic strain classification, resistance prediction, and cluster analysis (12 allele distance threshold). Factors associated with pre-XDR/XDR-TB were defined by odds ratios and a multivariate logistic regression model. Results: 1 017 MTBC strains were MDR, out of which 57.8 % (n=591) were pre-XDR, and 17.9 % (n=183) were XDR. Lineage 2 (L2) strains represented 41.7 % of the MDR, 77.2 % of the pre-XDR, and 86.3 % of the XDR strains, and were significantly associated with pre-XDR/XDR-TB (P < 0.001). Cluster rates were high among MDR (78 %) and pre-XDR/XDR (85 %) strains with three dominant L2 strain clusters (Cl 1-3) representing half of the pre-XDR and two thirds of the XDR-TB cases. Cl 1 strains accounted for 52.5 % of the XDR MTBC strains. Transmission could be confirmed by identical mutation patterns of particular pre-XDR/XDR strains. Conclusions: High rates of pre-XDR/XDR strains among MDR-TB patients require rapid changes in treatment and control strategies. Transmission of particular pre-XDR/XDR L2 strains is the main driver of the pre-XDR/XDR-TB epidemic. Accordingly, control of the epidemic in the region requires measures with stopping transmission esp. of pre-XDR/XDR L2 strains. Funding Statement: Parts of this work have been supported within the CRYPTIC consortium by the Bill & Melinda Gates Foundation [OPP1133541] and the Wellcome Trust [200205/Z/15/Z], the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy – EXC 2167 Precision Medicine in Inflammation, and the Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG). Declaration of Interests: None to declare. Ethics Approval Statement: Approval for the CRyPTIC study was obtained from the Health Ministry’s Screening Committee (HMSC), Government of India dated 6th October 2016. Approval was also obtained from the Institutional Ethics Committee (IEC) of The Foundation for Medical Research, Mumbai (Ref nos. FMR/IEC/TB/01a/2015 and FMR/IEC/TB/01b/2015) and Institutional Review Board of P.D. Hinduja Hospital and Medical Research Centre, Mumbai (Ref no. 915-15-CR [MRC]).

ТЕХНОЛОГИЯ ГЕНОДИАГНОСТИКИ BOVINE LEUKEMIA VIRUS У КРУПНОГО РОГАТОГО СКОТА, В ВЫРАБАТЫВАЕМОМ СЫРЬЕ И ПРОИЗВОДИМОЙ ПРОДУКЦИИ

The most important task of the dairy cattle industry is to obtain high quality raw milk. To achieve it, a set of measures is required, including aimed at increasing the biological safety of produced raw materials. The aim of the study was to create a scientific and methodological basis for the Bovine leukemia virus (BLV) gene diagnostics in a combined format of pathogen indication and identification. This required updating the strategy of BLV PCR-RFLP genotyping, consistent with its phylogenetic classification, taking into account the growing knowledge about the genetic diversity of 11 genotypes of the studied viral pathogen. When staging nested PCR, oligonucleotide primers were used, which initiate at the final stage of the reaction the production of a 444 bp env-gene fragment of the pathogen. Five restriction endonucleases were used in PCR-RFLP BLV genotyping of: PvuII, SspI, AsuHPI, HaeIII, and BstX2I. As a result of verification of the developed Bovine leukemia virus method for gene identification with an updated genotyping strategy, a technical result was obtained, expressed in the ability to identify all 11 BLV genotypes discovered to date by interpreting the generated 58 genotype-associated combinations of PCR-RFLP profiles.

Resolving phylogenetic and classical nomenclature: A Revision of Canarium Schumacher, 1817 (Mollusca, Neostromboidae, Strombidae)

This revision of the genus Canarium Schumacher, 1817 after Abbott (1960) advances our understanding of the phylogeny of Strombidae. Morphological characters were used to generate a phylogeny using maximum likelihood and including all of the recognised species. This resulted in the recognition of one tree, and within that tree the existing genera Canarium Schumacher, 1817 Tridentarius Kronenberg &amp; Vermeij, 2002 and Terestrombus Kronenberg &amp; Vermeij, 2002, and two more Maculastrombus n. gen. and Neostrombus n. gen. were recognisable clades. Furthermore, within the genus Canarium, four subgenera, Canarium (Canarium), Canarium (Conundrum), Canarium (Elegantum), and Canarium (Stereostrombus), were identified and described. We describe and define taxa that are compatible with the requirements of the International Code of Phylogenetic Nomenclature (PhyloCode 2020), and also conform to the requirements of the International Code of Zoological Nomenclature (ICZN 1999). This revision assists in generating a system of nomenclature that reflects the hypothetical relationships, and is at the same time practical in its application. We designate type localities and types for included species that were not yet addressed up until now.

Are the ICZN and PhyloCode that incompatible? A summary of the shifts in Stromboidean taxonomy and the definition of two new subfamilies in Stromboidae (Mollusca, Neostromboidae)

The taxonomy of Stromboideans has, historically, been simplistic. However, recent revisions have seen new taxa introduced to distinguish relationships between species clusters. We discuss these numerous advancements in Stromboidean systematics, and describe two new subfamilies here. The key diagnostic characteristic, the basal peg on the first lateral tooth, splits the Strombidae into two clades similar to those observed with molecular data. In defining the new subfamilies, Neoaligerinae and Neostrombinae, we demonstrate that the practical application of the International Code of Phylogenetic Nomenclature (PhyloCode 2020), can also conform to the requirements of the International Code of Zoological Nomenclature (ICZN 1999). This revision further advances and strengthens the framework of Stromboidean nomenclature such that it is able to reflect the current understanding of the evolutionary relationships between members of the Stromboidea.

Genetic diversity of avian leukosis virus subgroup J (ALV-J): toward a unified phylogenetic classification and nomenclature system

Avian leukosis virus subgroup J (ALV-J) has infected a variety of birds, causing major economic losses in China. Understanding the comprehensive criteria of classification and nomenclature of ALV-J would be useful for the investigation of the viral evolution and also for the prevention and control of this infection. An in-depth analysis of the genetic diversity of ALV-J was performed in the present study. Four hundred and seventy-five sequences of the gp85 gene, including thirteen of avian endogenous retrovirus designated ev/J and 462 of ALV-J, were used in the phylogenetic and the evolutionary distance analysis for this classification. The study identified that the current ALV-J strains were divided into two first-order clades (Clades 1 and 2) and three second-order clades (Clades 1.1, 1.2 and 1.3). The current Chinese ALV-J strains are predominantly in Clade 1.3, and the Chinese and Egyptian chicken flocks have been facing the emerging Clade 2 viruses. This system pioneers the classification efforts for ALV-J, which uses Pilot tree for rapid classification of the new isolates and also the addition of possible new clades. The proposed unified classification system will facilitate future studies of ALV-J epidemiology and genetic evolution and of the comparison of sequences obtained across the world.

Embryonic development of the fire-eye-tetra Moenkhausia oligolepis (Characiformes: Characidae)

SummaryThis study describes the embryonic development of Moenkhausia oligolepis in laboratory conditions. After fertilization, the embryos were collected every 10 min up to 2 h, then every 20 min up to 4 h, and afterwards every 30 min until hatching. The fertilized eggs of M. oligolepis measured approximately 0.85 ± 0.5 mm and had an adhesive surface. Embryonic development lasted 14 h at 25ºC through the zygote, cleavage, blastula, gastrula, neurula, and segmentation phases. Hatching occurred in embryos around the 30-somites stage. The present results contribute only the second description of embryonic development to a species from the Moenkhausia genus, being also the first for this species. Such data are of paramount importance considering the current conflicting state of this genus phylogenetic classification and may help taxonomic studies. Understanding the biology of a species that is easily managed in laboratory conditions and has an ornamental appeal may assist studies in its reproduction to both supply the aquarium market and help the species conservation in nature. Moreover, these data enable the use of M. oligolepis as a model species in biotechnological applications, such as the germ cell transplantation approach.

Re-purposing software for functional characterization of the microbiome

BackgroundWidespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the functionality of the microbial community, in order to characterize its currently or potentially active biological processes. Such functional analysis of metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we can directly compare sequencing reads to a functionally annotated database. However, since reads frequently match multiple sequences equally well, analyses benefit from a hierarchical annotation tree, e.g. for taxonomic classification where reads are assigned to the lowest taxonomic unit.ResultsTo facilitate functional microbiome analysis, we re-purpose well-known taxonomic classification tools to allow us to perform direct functional sequencing read classification with the added benefit of a functional hierarchy. To enable this, we develop and present a tree-shaped functional hierarchy representing the molecular function subset of the Gene Ontology annotation structure. We use this functional hierarchy to replace the standard phylogenetic taxonomy used by the classification tools and assign query sequences accurately to the lowest possible molecular function in the tree. We demonstrate this with simulated and experimental datasets, where we reveal new biological insights.ConclusionsWe demonstrate that improved functional classification of metagenomic sequencing reads is possible by re-purposing a range of taxonomic classification tools that are already well-established, in conjunction with either protein or nucleotide reference databases. We leverage the advances in speed, accuracy and efficiency that have been made for taxonomic classification and translate these benefits for the rapid functional classification of microbiomes. While we focus on a specific set of commonly used methods, the functional annotation approach has broad applicability across other sequence classification tools. We hope that re-purposing becomes a routine consideration during bioinformatic resource development.CWJ3S1nYSzUqUEQpCfrTiKVideo abstract

The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses

ABSTRACT The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as Arabidopsis, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in Solanum lycopersicum. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive cis-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.

Gallid Alphaherpesvirus 2 in the Egyptian Turkeys: Molecular Characterization and Establishment of a Universal System for Phylogenetic Classification

Introduction: Gallid alphaherpesvirus 2 (GaHV-2) is a highly contagious oncogenic virus that causes Marek’s disease in chickens and occasionally in turkeys. Among 100 genes identified in GaHV-2 genome, the Meq gene appears to involve viral virulence, oncogenicity, and genetic diversity. Despite the use of Meq gene sequences in phylogenetic classification of GaHV-2 strains circulating in many countries worldwide, no integrated system exists yet. Methods: Turkeys from 2 commercial Egyptian farms were presented with signs of dullness, dehydration, and emaciation. Samples prepared from the internal organs were examined by histopathology and immunohistochemistry. Pools of the internal organs were analyzed by PCR for identification of GaHV-2, avian leucosis virus, and reticuloendotheliosis virus. The Meq gene of an Egyptian strain was sequenced and analyzed in comparison to 40 reference strains for generation of a universal system for phylogenetic classification of GaHV-2 strains. Results: Gross and histopathological examination revealed grayish-white soft masses in the internal organs characterized by diffuse infiltration of pleomorphic neoplastic cells. All lymphoma cells were identified as T-lymphocytes of CD3+ phenotype. Samples of both farms were only positive for GaHV-2 by PCR. Sequence analysis of the Meq gene has classified the current turkey strain as related to the Egyptian strains identified in chicken in 2012. A universal phylogenetic system for classification of GaHV-2 strains into 4 clusters was proposed. The vaccine strains were all grouped in cluster 2, and most of the classical American strains belonged to cluster 4. Cluster 1 was further divided into 3 subclusters (1.1–1.3). Conclusion: GaHV-2 was identified in turkeys for the first time in Africa and the Middle East. Sequence analysis of the Meq gene of the Egyptian strain along with a wide array of the global strains has enabled the construction of a novel phylogenetic classification system.

Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends.

Background & objectives:Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India.Methods:The whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server.Results:Temporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b.Interpretation & conclusions:This study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.

Muscles of the male and female copulatory organs of Bursaphelenchus mucronatus and Chiloplacus sp. (Nematoda: Rhabditida).

Male and female copulatory organs figure prominently in nematode taxonomy, but the associated musculature remains insufficiently explored. The aim of this study was therefore to further our knowledge of the musculature of the vulva and male copulatory organs in nematodes by using phalloidin staining and confocal microscopy to examine two nematode species, Bursaphelenchus mucronatus and Chiloplacus sp. The musculature of the round vulva in Chiloplacus sp. comprises three pairs of radial vulval dilators and another pair of dilators of the anterior inner vulval plate. This arrangement is similar to that of the Rhabditida, but in Chiloplacus the anterior pair appears to have been transformed into the vulval plate muscles. The musculature of the slit-like vulva in B. mucronatus includes dilators of the vulval lips and external vulval flap, constrictors of the vulval slit and posterior transverse muscle bands. The opposing pairs of vulval dilators show quadrilateral symmetry as observed in the Rhabditida, but the constrictors running along the rim of the vulva have no counterparts in other species. The musculature of the male copulatory organ in Chiloplacus sp. comprises two pairs of spicule protractors and retractors and three pairs of gubernacular muscles. In B. mucronatus, as in the other Aphelenchoididae, the gubernaculum is absent and there is one pair of spicule protractors and two pairs of muscles inserted on the saddle (angular bend) of the spicules. The arrangement of the spicule saddle muscles resembles those of the gubernaculum, which may indicate that in this family the gubernaculum has become fused to the spicules. The literature review of muscles of nematode copulatory organs are given in a table for 15 muscle groups; it can be used for phylogenetic reconstruction and classification of the order Rhabditida.

Taxonomy, phylogeny and evolution of freshwater mussels (Unionoida: Unionoidea) in China revealed by multilocus phylogenetic analyses and mitochondrial phylogenomics

中国是东亚蚌类（蚌目：蚌超科）物种分布中心，共记录有26属.然而，在世界蚌目框架下，中国仍缺乏一个完整科学的蚌类分类系统.本研究基于多位点分子标记（COI、16S、28S）和线粒体基因组学重构聚焦于蚌超科的蚌目系统发育关系，ML、BI和BEAST系统发育结果均支持蚌科5亚科分类系统，即（（（Ambleminae+Gonideinae）+Rectidentinae）+Unioninae）+Parreysiinae；珍珠蚌科2亚科分类系统，即（Gibbosulinae+Margaritiferinae）；中国蚌类隶属蚌科4亚科（Gonideinae，Rectidentinae，Unioninae，Parreysiinae）13族和珍珠蚌科两亚科（Gibbosulinae，Margaritiferinae）.基于化石标定的分子钟显示：蚌科物种分化时间为中三叠世（median=232.07 Ma），其中雕刻蚌亚科（Parreysiinae）起源和物种分化时间早于其他亚科；矩形蚌亚科（Rectidentinae）物种分化时间最晚，为晚白垩世（median=94.72 Ma）；小方蚌亚科（Ambleminae）和隆脊蚌亚科（Gonideinae）最近共同祖先分化于晚侏罗纪世（median=144.69 Ma），珍珠蚌科起源于晚石炭世（median=312.61 Ma），物种分化于晚白垩世（median=91.59 Ma），中国蚌科现生物种最早起源时间可追溯到白垩纪（中国尖嵴蚌（Acuticosta chinensis），median=114.36 Ma）.蚌超科线粒体基因重排分析显示：蚌超科线粒体基因组有4种基因排列方式（GO），珍珠蚌科独享一种（GO1）；蚌科中Unioninae和Ambleminae共享一种（GO2）；Gonideinae有2种基因排列方式（GO3和GO4），其中室蚌（Chamberlainia hainesiana）独享一种（GO4），其余物种共享一种（GO3）.以往作为高阶元分类的贝壳形态、钩介幼虫形态以及育儿囊类型，并不能作为蚌科属及以上阶元分类依据.本研究重构了世界蚌目聚焦于蚌超科的系统发育关系和进化历史，建立了中国蚌类分类系统，为今后该类群区系多样性研究及资源保护提供了分类依据.;China is the most species-rich region for the Unionoidea (Unionidae + Margaritiferidae) in East Asia, with a total of 26 genera. However, in the context of global unionids, an integrated and scientific phylogenetic taxonomy for Chinese Unionoidea is still lack. Based on the multilocus molecular markers (COI, 16S, 28S) and mitochondrial genomics, we reconstructed the phylogenetic relationship of the Unionioda by focusing on the Unionoidea. All phylogenetic results of ML, BI and BEAST supported five monophyletic clades for subfamily levels within Unionidae, i.e. (((Ambleminae + Gonideinae) + Rectidentinae) + Unioninae) + Parreysiinae, and two subfamilies within Margaritiferidae, i.e. (Gibbosulinae + Margaritiferinae). Chinese Unionoidea belonged to four subfamilies (Gonideinae, Rectidentinae, Unioninae, Parreysiinae) thirteen tribes of Unionidae and 2 subfamilies (Gibbosulinae, Margaritiferinae) of Margaritiferidae. The fossil-calibrated molecular clock suggested the Unionidae species divergence at the Middle Triassic (median=232.07 Ma). The origin and species divergence time of the Parreysiinae were earlier than other subfamilies. The species divergence time of Rectidentinae was the latest among all subfamilies, at the Late Cretaceous (median=94.72 Ma). The most recently common ancestor of Ambleminae and Gonideinae diverged at the Late Jurassic (median=144.69 Ma). Margaritiferidae originated at the Late Carboniferous (median=312.61 Ma), and species divergence at the Late Cretaceous (median=91.59 Ma). The oldest living unionid species in China could be traced back to the Cretaceous (i.e. Acuticosta chinensis, median=114.36 Ma). Mitochondrial gene order (GO) analysis of the Unionoidea revealed that the presently published Unionoidea mitochondrial genome had four gene arrangements:one was exclusive to the Margaritiferidae (GO1); Unioninae and Ambleminae of Unionidae shared another one (GO2); Gonideinae had two gene arrangements (GO3 and GO4), of which was exclusive to Chamberlainia hainesiana (GO4). The morphological features of shells, glochidia and marsupium, which were used to high-level classification, could not be regarded as diagnostic features for the subfamily and the tribe level. This study reconstructed the phylogenetic relationship and evolutionary history of Unionoida worldwide and established complete systematics of Unionoidea in China, which providing the taxonomic basis for the diversity research and resource conservation of Chinese unionids.

Morphological and molecular assessment of the diversity of trematode communities in freshwater gastropods and bivalves in Los Tuxtlas tropical rainforest

Abstract Trematode life cycles involve molluscs as first intermediate hosts. The identification of trematodes based on the morphology of cercariae released from molluscs is challenging because the identification relies on adult forms obtained from their definitive hosts. Several studies have recently genetically characterized these larval forms establishing a link with adults sampled from their vertebrate hosts, allowing their identification at species level. In Los Tuxtlas tropical rainforest, in south-eastern Mexico, 57 species of trematodes have been reported from wildlife vertebrates; however, studies evaluating the diversity of trematode cercariae in molluscs are lacking. Here, we studied 11 species of molluscs to assess the diversity of cercariae in two lakes of Los Tuxtlas, Veracruz, Mexico; six of the 11 species were infected. Twelve cercarial morphotypes were collected and characterized morphologically. Sequences of the 28S ribosomal RNA gene were generated to allocate each morphotype into a family using the most recent phylogenetic classification of the Digenea as a framework; molecular work revealed 16 genetic lineages; some cercariae were identified up to genus (Apharyngostrigea, Ascocotyle, Centrocestus, Echinochasmus, Lecithodendrium and Posthodiplostomum), and some to species levels (Gorgoderina rosamondae, Langeronia macrocirra, Oligogonotylus manteri and Phyllodistomum inecoli) based on their phylogenetic position within the tree, and the genetic distance with respect to other sequenced congeners. Therefore, the cercarial morphotypes in the present study represent at least 16 putative species. Our study contributes to a better understanding of the trematode diversity in an area of high vertebrate species diversity, and to the knowledge of trematode life cycles.

Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies.

Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.

Genetic and functional diversity of PsyI/PsyR quorum-sensing system in the Pseudomonas syringae complex.

Strains belonging to the Pseudomonas syringae complex often possess quorum-sensing systems that comprise N-acyl-l-homoserine lactone (AHL) synthases (PsyI) and AHL receptors (PsyR). Here, we investigated the diversity of PsyI/PsyR quorum-sensing systems in 630 strains of the P. syringae complex. AHL production was observed in most strains of Pseudomonas amygdali and Pseudomonas meliae, and a few strains of Pseudomonas coronafaciens and P. syringae. The DNA sequences of psyIR and their upstream and downstream regions were categorized into eight types. P. amygdali pv. myricae, Pseudomonas savastanoi, and P. syringae pv. solidagae, maculicola, broussonetiae, and tomato encoded psyI, but did not produce detectable amounts of AHL. In P. savastanoi, an amino acid substitution (R27S) in PsyI caused defective AHL production. The psyI gene of P. syringae pv. tomato was converted to pseudogenes by frameshift mutations. Escherichia coli harboring psyI genes from P. amygdali pv. myricae, P. syringae pv. solidagae and broussonetiae showed high levels of AHL production. Forced expression of functional psyR restored AHL production in P. amygdali pv. myricae and P. syringae pv. solidagae. In conclusion, our study indicates that the PsyI/PsyR quorum-sensing systems in P. syringae strains are genetically and functionally diverse, with diversity being linked to phylogenetic and pathovar classifications.

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses.

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.