Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates

Nematology ◽  
2019 ◽  
Vol 21 (5) ◽  
pp. 533-546 ◽  
Author(s):  
Dana K. Howe ◽  
McKinley Smith ◽  
Danielle M. Tom ◽  
Amanda M.V. Brown ◽  
Amy B. Peetz ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Markers ◽  
Species Complex ◽  
Evolutionary Rates ◽  
Biological Processes ◽  
Bacterial Symbionts ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Phylogenetic Resolution ◽  
Variable Evolutionary Rates

Summary Bacterial symbioses play important roles in shaping diverse biological processes in nematodes, and serve as targets in nematode biocontrol strategies. Focusing on the Xiphinema americanum species complex, we expanded upon recent research investigating patterns of coevolution between Xiphinema spp. and Xiphinematobacter spp., utilising two symbiont genetic markers of varying evolutionary rates. Phylogenetic analysis of nematode mitochondrial DNA (mtDNA) revealed five strongly supported major clades. Analysis of slow-evolving 16S rDNA in bacterial symbionts resulted in a phylogenetic topology composed of four major clades that grouped taxa highly congruent with the nematode mtDNA topology. A faster evolving protein-coding symbiont gene (nad) provided more phylogenetic resolution with seven well-supported clades, also congruent with the nematode mtDNA tree topology. Our results reinforce recent studies suggesting extensive coevolution between Xiphinema spp. and their vertically transmitted endosymbionts Xiphinematobacter spp. and illustrate the advantages of including genetic markers of varying evolutionary rates in coevolutionary and phylogenetic studies.

scholarly journals Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers’ Mitochondrial Phylogenomics

2021 ◽  
Vol 22 (11) ◽  
pp. 5586
Author(s):  
Deqiang Ai ◽  
Lingfei Peng ◽  
Daozheng Qin ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Rates ◽  
Compositional Heterogeneity ◽  
Heterogeneous Mixture ◽  
Phylogenetic Studies ◽  
Homogeneous Models ◽  
Complete Mitogenome ◽  
A Site ◽  
Variable Evolutionary Rates ◽  
First Time

Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers' phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.

scholarly journals Mitochondrial DNA-like sequence in the nuclear genome of Saguinus (Callitrichinae, Primates): transfer estimation

2000 ◽  
Vol 23 (1) ◽  
pp. 35-42
Author(s):  
Marcelo Vallinoto ◽  
Leonardo Sena ◽  
Iracilda Sampaio ◽  
Horacio Schneider ◽  
Maria Paula Schneider
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Phylogenetic Analyses ◽  
Nuclear Genome ◽  
Mitochondrial Genes ◽  
Evolutionary Rates ◽  
Stop Codons ◽  
Phylogenetic Resolution ◽  
Mitochondrial Sequences

Mitochondrial DNA-like sequences have been found in the nuclei of a variety of organisms. These nuclear pseudogenes can be used to estimate relative evolutionary rates of mitochondrial genes, and can be used as outgroups in phylogenetic analyses. In this study, mitochondrial sequences with pseudogene-like characteristics, including deletions and/or insertions and stop codons, were found in tamarins (Saguinus spp., Callitrichinae, Primates). Phylogenetic analysis allowed estimation of the timing of the migration of these sequences to the nuclear genome, and also permitted inferences on the phylogeny of the genus. The choice of an inadequate outgroup (Aotus infulatus) prevented a good phylogenetic resolution of the subfamily Callitrichinae. The relatively ancient divergence of the Cebidae (Callitrichinae, Aotinae and Cebinae) may have favored confounding homoplasies.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Re-Evaluation of the Podosphaera tridactyla Species Complex in Australia

2021 ◽  
Vol 7 (3) ◽  
pp. 171
Author(s):  
Reannon L. Smith ◽  
Tom W. May ◽  
Jatinder Kaur ◽  
Tim I. Sawbridge ◽  
Ross C. Mann ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Species Complex ◽  
Taxonomic Revision ◽  
Stone Fruit ◽  
Prunus Species ◽  
Wide Range ◽  
Unidentified Species ◽  
The Rose ◽  
Generation Sequencing

The Podosphaera tridactyla species complex is highly variable morphologically and causes powdery mildew on a wide range of Prunus species, including stone fruit. A taxonomic revision of the Po. tridactyla species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host matK chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental Prunus species accessioned as Po. tridactyla or Oidium sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using matK phylogenetic analysis, which identified that four had been misidentified as Prunus but were actually Malusprunifolia. Podosphaera species were identified using ITS+28S phylogenetic analysis, recognising three Podosphaera species on stone fruit and related ornamental Prunus hosts in Australia. These were Po.pannosa, the rose powdery mildew, and two species in the Po. tridactyla species complex: Po. ampla, which was the predominant species, and a previously unidentified species from peach, which we describe here as Po. cunningtonii.

scholarly journals Upregulation of LINC01426 promotes the progression and stemness in lung adenocarcinoma by enhancing the level of SHH protein to activate the hedgehog pathway

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Xiaoli Liu ◽  
Zuwei Yin ◽  
Linping Xu ◽  
Huaimin Liu ◽  
Lifeng Jiang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Bioinformatics Analysis ◽  
Epithelial Mesenchymal Transition ◽  
Mrna Level ◽  
Hedgehog Pathway ◽  
Biological Processes ◽  
Protein Coding ◽  
Mesenchymal Transition ◽  
Functional Roles ◽  
Rip Assay

AbstractLong noncoding RNAs (lncRNAs) play crucial roles in regulating a variety of biological processes in lung adenocarcinoma (LUAD). In our study, we mainly explored the functional roles of a novel lncRNA long intergenic non-protein coding RNA 1426 (LINC01426) in LUAD. We applied bioinformatics analysis to find the expression of LINC01426 was upregulated in LUAD tissue. Functionally, silencing of LINC01426 obviously suppressed the proliferation, migration, epithelial–mesenchymal transition (EMT), and stemness of LUAD cells. Then, we observed that LINC01426 functioned through the hedgehog pathway in LUAD. The effect of LINC01426 knockdown could be fully reversed by adding hedgehog pathway activator SAG. In addition, we proved that LINC01426 could not affect SHH transcription and its mRNA level. Pull-down sliver staining and RIP assay revealed that LINC01426 could interact with USP22. Ubiquitination assays manifested that LINC01426 and USP22 modulated SHH ubiquitination levels. Rescue assays verified that SHH overexpression rescued the cell growth, migration, and stemness suppressed by LINC01426 silencing. In conclusion, LINC01426 promotes LUAD progression by recruiting USP22 to stabilize SHH protein and thus activate the hedgehog pathway.

scholarly journals Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 326
Author(s):  
Yu-Jun Wang ◽  
Hua-Ling Wang ◽  
Xiao-Wei Wang ◽  
Shu-Sheng Liu
Keyword(s):  
Gene Expression ◽  
Slow Rate ◽  
Species Complex ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Species Comparisons ◽  
Differential Gene ◽  
Males And Females ◽  
And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

scholarly journals Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05

2010 ◽  
Vol 11 (3) ◽  
pp. 243
Author(s):  
Saber Jelokhani-Niaraki ◽  
Majid Esmaelizad ◽  
Morteza Daliri ◽  
Rasoul Vaez-Torshizi ◽  
Morteza Kamalzadeh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Protein Coding ◽  
Coding Regions ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Subtype A ◽  
Virus Subtype

Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing

2018 ◽  
Vol 57 (7) ◽  
pp. 905-908 ◽  
Author(s):  
David New ◽  
Alicia G Beukers ◽  
Sarah E Kidd ◽  
Adam J Merritt ◽  
Kerry Weeks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sporothrix Schenckii ◽  
Sensu Stricto ◽  
Northern Territory ◽  
Whole Genome ◽  
Phylogenetic Resolution ◽  
Genetic Clustering ◽  
Multiple Species

AbstractWhole genome sequencing (WGS) was used to demonstrate the wide genetic variability within Sporothrix schenckii sensu lato and establish that there are two main species of Sporothrix within Australian clinical isolates—S. schenckii sensu stricto and Sporothrix globosa. We also demonstrated southwest Western Australia contained genetically similar S. schenckii ss strains that are distinct from strains isolated in the eastern and northern states of Australia. Some genetic clustering by region was also noted for northern NSW, Queensland, and Northern Territory. Phylogenetic analysis of WGS data provided greater phylogenetic resolution compared to analysis of the calmodulin gene alone.

scholarly journals The evolution of the metazoan Toll receptor family and its expression during protostome development

2021 ◽  
Author(s):  
Andrea Orús-Alcalde ◽  
Tsai-Ming Lu ◽  
Andreas Hejnol
Keyword(s):  
Phylogenetic Analysis ◽  
Transmembrane Domain ◽  
Leucine Rich Repeat ◽  
Animal Development ◽  
Phylogenetic Studies ◽  
Repeat Domain ◽  
Toll Receptor ◽  
P Type

Abstract Background: Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa.Results: We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.Conclusions: Our findings suggest that the bilaterian TLRs likely emerged by duplication from a single TLR encoding gene (proto-TLR) present in the last common cnidarian-bilaterian ancestor. This proto-TLR gene duplicated before the split of protostomes and deuterostomes; a second duplication occurred in the lineage to the Trochozoa. While all three clades further radiated in several spiralian lineages, specific TLRs clades have been presumably lost in others. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests their involvement in immunity and development.

scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

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