Comprehensive Phylogenetic Tree Research Articles

Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting – a relatively rare nest construction phenotype in birds – was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data.

Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.

Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data.

Single-cell DNA sequencing enables the construction of evolutionary trees that can reveal how tumors gain mutations and grow. Different whole-genome amplification procedures render genomic materials of different characteristics, often suitable for the detection of either single-nucleotide variation or copy number aberration, but not ideally for both. Consequently, this hinders the inference of a comprehensive phylogenetic tree and limits opportunities to investigate the interplay of SNVs and CNAs. Existing methods such as SCARLET and COMPASS require that the SNVs and CNAs are detected from the same sets of cells, which is technically challenging. Here we present a novel computational tool, SCsnvcna, that places SNVs on a tree inferred from CNA signals, whereas the sets of cells rendering the SNVs and CNAs are independent, offering a more practical solution in terms of the technical challenges. SCsnvcna is a Bayesian probabilistic model using both the genotype constraints on the tree and the cellular prevalence to search the optimal solution. Comprehensive simulations and comparison with seven state-of-the-art methods show that SCsnvcna is robust and accurate in a variety of circumstances. Particularly, SCsnvcna most frequently produces the lowest error rates, with ability to scale to a wide range of numerical values for leaf nodes in the tree, SNVs, and SNV cells. The application of SCsnvcna to two published colorectal cancer data sets shows highly consistent placement of SNV cells and SNVs with the original study while also supporting a refined placement of ATP7B, illustrating SCsnvcna's value in analyzing complex multitumor samples.

Sequencing report of the rRNA amplicons of Echinochloa crus-galli in Iraq

This study was conducted to identify the genetic polymorphisms of one wild grass sample species and assess the phylogenetic distribution these isolates occupy based on their internal transcribed (ITS) ribosomal sequences. This study amplified one genetic locus covering a portion of the ITS rRNA sequences. A direct sequencing strategy was performed for the observed PCR amplicons in the amplified genetic locus. Subsequently, a comprehensive phylogenetic tree was constructed in the observed variants for these sequences to reveal the accurate phylogenetic distances alongside other relative sequences. Our results indicated the identity of the investigated wild grass samples (assigned S1 and S2). Sequencing reactions indicated that our investigated samples belonged to Echinochloa crusgalli var. crus-galli (panicum grass), a common wild grass dominated in tropical Asia. Two ribosomal variations were identified in the investigated wild grass samples, 61C>T, observed in the S2 sample and 408C>A, observed in both the S1 and S2 samples. According to the identified results, the investigated samples were positioned within one distinct phylogenetic clade of these identified wild grass sequences in the currently generated comprehensive tree. These positionings were observed within the main clade of Echinochloa crus-galli. Based on the identified ribosomal sequences, it was found that the currently investigated samples may exhibit variable extents of diversities originating from several Asian and South American ancestors. Also, the currently constructed tree revealed that the investigated wild grass sequences belonged to one distinct clade of Echinochloa crus-galli, having many sequences of close phylogenetic connections. This clade occupied far away phylogenetic positions from the other comparable grasses within the same tree. Keywords: rRNA amplicons, Echinochloa crus-galli, Rice

A Rare Fish Amphistome Revisited: The Phylogenetic Position of Kalitrema kalitrema (Trematoda: Cladorchiidae) Found in Hypostomus spp. (Siluriformes: Loricariidae) from Brazil

Despite recent advances in the molecular knowledge of amphistome trematodes, most genera known from fish remain to be genetically characterized. This is the case for Kalitrema, a genus of the speciose family Cladorchiidae and the type of Kalitrematinae. The type and only species of this genus, Kalitrema kalitrema Travassos, 1933, was originally proposed based on two specimens found in an armored suckermouth catfish from Brazil, and its phylogenetic position has not been evaluated. In this study, paramphistomes found in Hypostomus alatus (2/9; 22.2%) and Hypostomus francisci (4/143; 2.8%) from the Paraobepa River (São Francisco River basin), Minas Gerais, Brazil, between December 2019 and November 2021, were subjected to morphological study. The parasites were identified in low intensity of infection [1.2 (1–2)] and redescribed as K. kalitrema. This species exhibits unique features such as a linguiform body with a circular ridge near the anterior end and a deep, median notch present at the posterior extremity of the body, apparently dividing the body into two lobes. A subset of specimens was further subject to phylogenetic analyses based on the most densely sampled markers, the nuclear ribosomal RNA (28S and ITS2) and mitochondrial cox1, which revealed the inclusion of K. kalitrema in a Neotropical clade of fish paramphistomes. The most comprehensive phylogenetic tree, based on the 28S dataset, confirmed K. kalitrema as an independent, early diverging lineage among Neotropical fish cladorchiids. However, the monophyly of Kalitrematinae was not sustained, given that species of the other kalitrematine genera Pseudocladorchis and Iquitostrema included in the phylogenetic analysis fell in a distinct clade with other fish cladorchiids. As a result, we propose here a narrower concept for Kalitrematinae sensu stricto, accommodating only Kalitrema (type genus) until a more natural subfamilial or familial classification is provided.

Phylogenetic relationships and diversification dynamics of Cerastium (Alsineae: Caryophyllaceae): implications for biogeographical patterns of herbs in the Northern Hemisphere

Abstract The evolutionary history of herbaceous species in the Northern Hemisphere remains poorly understood. The genus Cerastium is one of the most species-rich herbaceous genera in the Alsineae (Caryophyllaceae), and is mainly distributed in the Northern Hemisphere. Thus, it provides an ideal opportunity to explore the biogeographical history of herbs in the Northern Hemisphere. Here, we present a comprehensive phylogenetic tree for Cerastium with 75 species based on one nuclear and five plastid DNA markers. We then use an integrated phylogenetic, molecular dating, biogeographical, and diversification rate method to examine the spatiotemporal evolution of Cerastium. Cerastium is strongly supported as monophyletic and contains three major clades (Orthodon, Strephodon, and C. fragillimum). Cerastium originated from Europe in the middle Miocene (c. 13.45 million years ago), and subsequently colonized the New World, Africa, Asia, and Australasia through multiple intercontinental dispersal events. The dispersal of Cerastium from Europe (to both the East and West) and subsequent diversifications contributed to the formation of its contemporary Holarctic distribution pattern. The genus experienced rapid lineage accumulation during the late Miocene, possibly coinciding with a global decrease in temperature. These findings highlight the importance of the Northern Hemisphere in herbaceous species diversification in the late Miocene and Pliocene, and will deepen our understanding of the evolution of herbaceous plants.

Appendage-Bearing Sordariomycetes from Dipterocarpus alatus Leaf Litter in Thailand.

Leaf litter is an essential functional aspect of forest ecosystems, acting as a source of organic matter, a protective layer in forest soils, and a nurturing habitat for micro- and macro-organisms. Through their successional occurrence, litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling. Despite their importance in terrestrial ecosystems and their abundance and diversity, information on the taxonomy, diversity, and host preference of these decomposer taxa is scarce. This study aims to clarify the taxonomy and phylogeny of four saprobic fungal taxa inhabiting Dipterocarpus alatus leaf litter. Leaf litter samples were collected from Doi Inthanon National Park in Chiang Mai, northern Thailand. Fungal isolates were characterized based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, tef1-α, rpb2). One novel saprobic species, Ciliochorella dipterocarpi, and two new host records, Pestalotiopsis dracontomelon and Robillarda australiana, are introduced. The newly described taxa are compared with similar species, and comprehensive descriptions, micrographs, and phylogenetic trees are provided.

Itol.toolkit accelerates working with iTOL (Interactive Tree Of Life) by an automated generation of annotation files.

iTOL is a powerful and comprehensive phylogenetic tree visualization engine. However, adjusting to new templates can be time-consuming, especially when many templates are available. We developed an R package namely itol.toolkit to help users generate all 23 types of annotation files in iTOL. This R package also provides an all-in-one data structure to store data and themes, accelerating the step from metadata to annotation files of iTOL visualizations through automatic workflows. The manual and source code are available at https://github.com/TongZhou2017/itol.toolkit. Supplementary data are available at Bioinformatics online.

Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation.

Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].

Abstract 213: Phylogenetic reconstruction across 303 metastatic tumor samples using Ultima whole-genome sequencing dramatically increases subclonal resolution

Abstract Comprehensive characterization of tumor evolution is essential for understanding the drivers of metastasis and treatment resistance, which are still largely unknown. Studying evolution and resistance requires large cohorts of patients; for each patient, a comprehensive phylogenetic tree is used to follow clones over time and space. Deep whole-genome sequencing (WGS) enables the creation of more robust phylogenies, since (i) each clone is characterized by far more clone-specific mutations (compared to whole-exome or panel sequencing); and (ii) WGS yields more accurate clonal and sub-clonal allelic copy-number estimates, enabling more precise estimation of the fraction of cancer cells that harbor each mutation. Due to recent development of more affordable WGS by Ultima Genomics, we set out to test our ability to construct phylogenetic trees based on Ultima WGS. Ultima sequencing has demonstrated high sensitivity and specificity for detecting germline polymorphisms, but its performance on somatic mutation calling has not yet been rigorously studied. First, we adjusted our somatic mutation detection pipeline to work with Ultima-generated WGS data and tested its performance using well-studied cell line tumor/normal pairs. We assembled a ground truth set of somatic mutations based on deep sequencing data from multiple platforms for the breast cancer cell line pairs (HCC1954/HCC1954-BL and HCC1143/HCC1143-BL) and the melanoma tumor/normal cell line pair (COLO829/COLO829-BL). We found that mutation detection performance was on-par with other platforms for single nucleotide variations. Next, we identified 32 patients from various cancer types (breast, lung, cholangiocarcinoma, and melanoma) treated with a variety of therapies. We collected between 4 to 14 samples per patient at autopsy (total of 303), and sequenced them with Ultima to an average coverage of 63x (range 48x-91x). We identified mutations using our Ultima-adjusted WGS pipeline and constructed phylogenetic trees using our PhylogicNDT suite of tools. We then compared the results to trees previously constructed from mostly whole-exomes (and a few whole-genomes) sequenced on Illumina. We demonstrate that the trees generated from Ultima WGS data are consistent with the previously generated trees, and proved to be much more detailed. At commercialization, we anticipate that WGS for projects like this will be performed at ~1/6th the cost of current NGS offerings (on par with current WES costs). Therefore, it will enable larger studies and more accurate phylogenetic reconstruction, which will advance the study of tumor evolution and resistance. Citation Format: Julian Hess, Elizabeth Martin, Ilya Soifer, Hila Benjamin, Mendy Miller, Carrie Cibulskis, Brian P. Danysh, Matthew Coole, Stacey Gabriel, Dejan Juric, Doron Lipson, Gad Getz. Phylogenetic reconstruction across 303 metastatic tumor samples using Ultima whole-genome sequencing dramatically increases subclonal resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 213.

Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers.

The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.

Mitochondrial genome of Acheilognathusbarbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis.

Acheilognathusbarbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A.barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasboraparva. The complete length of the mitochondrial genome of A.barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasboraparva as the outgroup. Acheilognathusbarbatulus, Acheilognathustonkinensis and Acheilognathuscf.macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.

Two New Records of Agaricales (Psilocybe papuana and Cystoagaricus populinus) from China

T wo new records of agaric macrofungi, Cystoagaricus populinus and Psilocybe papuana, are described from Northeast and Southwest China. Morphological characteristics were examined and a phylogenetic tree was constructed. Cystoagaricus populinus is characterized by orange-brown pileus and pileipellis. Additionally, the significant characteristics of P. papuana are brown with umbo pileus, and basidiospores with germ pores. The phylogenetic analyses based on the ITS region indicated that these two species were most closely related to C. populinus and Psilocybe cf. papuana, respectively. Prior to this study, P. papuana distributed found in Papua New Guinea, while C. populinus found in Italy and Spain. Comprehensive descriptions, illustrations, hand drawings and phylogenetic trees of C. populinus and P. papuana are provided.

Sequencing of the ribosomal AMP icons of six species belonged to two families of Poaceae and Cyperaceae

This study was conducted to identify the genetic polymorphisms of sixspecies (assigned S1 to S4and S10 to S11) isolated from two different families, Poaceae (S1 to S4) and Cyperaceae (S10 and S11), one genetic locus covering a portion of the internal transcribed spacer 1 (ITS1), 5.8S ribosomal RNA gene, and internal transcribed spacer 2 (ITS2) sequences were amplified in this study. A direct sequencing strategy was performed for the observed PCR amplicons in the amplified genetic locus. Subsequently, a comprehensive phylogenetic tree was constructed in the observed variants to assess the accurate phylogenetic distances alongside relative sample sequences for each investigated family. Our results indicated the presence of variable homology between our investigated species of the corresponding families. Sequencing results showed the presence of four variants distributed in some of the investigated samples (S4 and S9). According to phylogenetic data for each constructed tree, the investigated samples in each tree were positioned in a phylogenetic clade corresponding to its family. These positions were represented by many incorporated organisms with a variety of genetic distances. Most of the clades were positioned in distinctly separated places from each other in the tree. Based on the utilized ITS amplicons, it was made clear that almost all investigated samples were originated from variable Asian sources, while other investigated samples exhibited multi-geographical origins. These different positions were generated due to several ancestral differences found in the pattern and extent of the observed nucleic acid variations in the analyzed families

Global phylogenetic analysis of the RNA-dependent RNA polymerase with OrViT (OrthornaVirae Tree)

Viruses of the kingdom Orthornavirae are the causative agents of many diseases in humans, animals and plants and play an important role in the ecology of the biosphere. Novel orthornaviral viral sequences are constantly being discovered from environmental datasets, but generating high-quality and comprehensive phylogenetic trees of Orthornavirae to resolve their taxonomic and phylogenetic relationships is still a challenge. To assist microbial ecologists and virologists with this task, we developed OrViT (OrthornaVirae Tree), a pipeline that integrates and updates published methods and bridges various public software to generate a global phylogenetic tree of the RNA-dependent RNA polymerase (RdRp) encoded by all orthornaviral genomes. The pipeline can infer the phylogenetic relationships between RdRp sequences extracted from the RefSeq viral database and the users’ own assembled contigs or protein datasets. The results from OrViT can be used for the taxonomic identification of novel viruses and suggest revisions of the existing phylogeny of RNA viruses. OrViT includes several Perl and Bash scripts assembled into a Makefile, making it portable between different Linux-based operating systems and easy to use. OrViT is freely available from https://github.com/chengdongqiang/OrViT.

Global variation in diversification rate and species richness are unlinked in plants

Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.

The Multifaceted Roles of Fungal Cutinases during Infection.

Cuticles cover the aerial epidermis cells of terrestrial plants and thus represent the first line of defence against invading pathogens, which must overcome this hydrophobic barrier to colonise the inner cells of the host plant. The cuticle is largely built from the cutin polymer, which consists of C16 and C18 fatty acids attached to a glycerol backbone that are further modified with terminal and mid-chain hydroxyl, epoxy, and carboxy groups, all cross-linked by ester bonds. To breach the cuticle barrier, pathogenic fungal species employ cutinases—extracellular secreted enzymes with the capacity to hydrolyse the ester linkages between cutin monomers. Herein, we explore the multifaceted roles that fungal cutinases play during the major four stages of infection: (i) spore landing and adhesion to the host plant cuticle; (ii) spore germination on the host plant cuticle; (iii) spore germ tube elongation and the formation of penetrating structures; and (iv) penetration of the host plant cuticle and inner tissue colonisation. Using previous evidence from the literature and a comprehensive molecular phylogenetic tree of cutinases, we discuss the notion whether the lifestyle of a given fungal species can predict the activity nature of its cutinases.

Molecular Study of Eimeria species in Quail birds (Coturnix coturnix japonica) in Thi-Qar Province, Southern Iraq

Fecal samples were collected from 330 quail birds from different areas of Thi-Qar province, Iraq. Allsamples were examined by traditional laboratory methods. Four species of Eimeria were diagnosed inquail (Eimeria bateri, Eimeria uzura, Eimeria tsunodai and Eimeria fluminensis), with a total infectionwas 64.54% (213 out of 330). DNA was extracted from 100 positive samples confirm the small subunitrRNA (18s) gene by Polymerase chain reaction using a general primer for Eimeria species, Sevengenotypes were according to the identify of DNA sequences of Eimeria species in Japanese quail, theaccession codes to NCBI-Genbank. using A comprehensive phylogenetic tree was generated in thepresent study, this details were being analyzed. This was the first molecular study in Iraq for Eimeriain common quail.

Identifying a Novel Bile Salt Hydrolase from the Keystone Gut Bacterium Christensenella minuta.

Christensenella minuta are human gut dwelling bacteria that have been proposed as key members of the gut microbiome, regulating energy balance and adiposity of their host. We formerly identified that a novel strain of C. minuta (strain DSM33407) boosted microbiota diversity and stimulated deconjugation of the primary bile acid taurocholic acid in human samples. However, there is no description of a bile salt hydrolase (BSH) protein carried in the genome of C. minuta. Here, we identified and cloned a protein from C. minuta’s genome that carries a potent BSH activity, which preferentially deconjugates glycine-conjugated bile acids. We then retrieved 14,319 putative BSH sequences from the NCBI database and filtered them using the UHGP database to collect a total of 6701 sequences that were used to build the most comprehensive phylogenetic tree of BSH-related enzymes identified in the human microbiome so far. This phylogenetic tree revealed that C. minuta’s BSH amino acid sequence clusters away from others with a threshold of 70% identity. This is therefore the first description of C. minuta’s BSH protein, which may be involved in its unique role within the human gut microbial ecosystem.

Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)

Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.