Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data

SummaryVirtually all aphids maintain an obligate mutualistic symbiosis with bacteria from theBuchneragenus, which produce essential nutrients for their aphid hosts. Most aphids from the Lachninae subfamily have been consistently found to house additional endosymbionts, mainlySerratia symbiotica. This apparent dependence on secondary endosymbionts was proposed to have been triggered by the loss of the riboflavin biosynthetic capability byBuchnerain the Lachninae last common ancestor. However, an integral large-scale analysis of secondary endosymbionts in the Lachninae is still missing, hampering the interpretation of the evolutionary and genomic analyses of these endosymbionts. Here, we analysed the endosymbionts of selected representatives from seven different Lachninae genera and nineteen species, spanning four tribes, both by FISH (exploring the symbionts’ morphology and tissue tropism) and 16S rRNA gene sequencing. We demonstrate that all analysed aphids possess dual symbiotic systems, and while most harbourS. symbiotica, some have undergone symbiont replacement by other phylogenetically-distinct bacterial taxa. We found that these secondary associates display contrasting cell shapes and tissue tropism, and some appear to be lineage-specific. a scenario for symbiont establishment in the Lachninae, followed by changes in the symbiont’s tissue tropism and symbiont replacement events, thereby highlighting the extraordinary versatility of host-symbiont interactions.Originality-Significance StatementA key question in evolutionary biology is that of how mutualism evolves. One way to approach this problem is to investigate recently-established mutualistic associations, particularly by comparing various symbiotic systems in closely related hosts. Here, we present a most comprehensive study to investigate co-obligate symbioses in aphids, focusing in the Lachninae subfamily. While most aphids keep an obligate vertically-transmitted association with intracellularBuchnerabacteria, some, such as members of the Lachninae subfamily, host an additional putative co-obligate symbiont. Thus, the Lachninae dual symbiotic systems offer a unique opportunity to understand the evolutionary dynamics of host-symbiont associations, in particularly how secondary symbionts become obligate and eventually may be replaced. Through genome sequencing of three aphid species belonging to distantly related tribes within the subfamily, we have previously corroborated that they have indeed established co-obligate mutualistic associations with theS. symbioticasecondary endosymbiotic bacterium. This was putatively facilitated by an ancient pseudogenisation of the riboflavin biosynthetic pathway inBuchnera, rendering it unable to provide the essential vitamin to the host. However, not all Lachninae members harbourS. symbiotica, some species being associated to at least four different bacterial taxa. To correctly interpret the genomic data and to understand the evolutionary dynamics of these symbiotic associations, a wide-range analysis of both the phylogenetic relations as well as of the secondary symbionts’ localisation within the bacteriome is needed. To tackle this, we have combined phylogenetic analyses of the symbionts’ 16S rRNA gene sequences and FISH microscopy, to understand the symbiont’s identity as well as the morphological characteristics and tissue tropism. The phylogenetic affinities and patterns of co-divergence of the symbionts, in combination with previously published genomic data, have enabled us to build an evolutionary scenario for the establishment, changes in tissue tropism such as “stable” internalisation into bacteriocytes, and replacements of the putative “ancient” secondary endosymbiont from the Lachninae last common ancestor. Also, we were able to determine through phylogenetic analyses that some putative co-obligate endosymbionts may have evolved from once facultative ones. The evolutionary framework presented here reveals a dynamic pattern for the more recent evolutionary history of these symbioses, including replacement and novel acquisition of phylogenetically different co-obligate symbionts. This study opens new research avenues on this symbiont-diverse subfamily, providing insight into how mutualism in endosymbiotic associations can evolve, and the role these bacteria have played in the species’ adaptation and even in the speciation process.

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The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera

Genes ◽

10.3390/genes10020108 ◽

2019 ◽

Vol 10 (2) ◽

pp. 108 ◽

Cited By ~ 3

Author(s):

Nan Song ◽

Xin-xin Li ◽

Qing Zhai ◽

Hakan Bozdoğan ◽

Xin-ming Yin

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Genomic Data ◽

Considerable Progress ◽

Mitochondrial Genomes ◽

Special Focus ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Taxonomic Sampling ◽

Inference Methods

The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.

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Population genomic evidence for radiative divergence of four Orychophragmus (Brassicaceae) species in eastern Asia

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz026 ◽

2019 ◽

Vol 191 (1) ◽

pp. 18-29 ◽

Cited By ~ 1

Author(s):

Linling Zhong ◽

Huanhuan Liu ◽

Dafu Ru ◽

Huan Hu ◽

Quanjun Hu

Keyword(s):

Statistical Tests ◽

Phylogenetic Analyses ◽

Genomic Data ◽

Gene Trees ◽

Eastern Asia ◽

Interspecific Relationships ◽

Population Genomic ◽

Interspecific Divergence ◽

Alternative Hypotheses ◽

Genetic Clusters

Abstract Radiation rather than bifurcating divergence has been inferred through a number of phylogenetic analyses using different DNA fragments. However, such inferences have rarely been tested by examining alternative hypotheses based on population genomic data. In this study, we sequenced the transcriptomes of 32 individuals from 13 populations of four Orychophragmus spp. (Brassicaceae) to investigate their divergence history. Cluster and population structure analyses recovered four distinct genetic clusters without any genetic mixture. Most orthologous genes produced unresolved bifurcating interspecific relationships with a star phylogeny. The resolved gene trees were highly inconsistent with each another in reconstructing interspecific relationships. Population genomic analyses suggested unexpectedly high genetic divergence and a lack of gene flow between the four species. We examined radiation vs. bifurcating divergence between these four species based on coalescent modelling tests of population genomic data. Our statistical tests supported a radiation of these species from a common ancestor at almost the same time, rejecting stepwise bifurcating interspecific divergence with time. This nearly simultaneous radiation was dated to the Quaternary, during which climate changes are suggested to have promoted species diversity in eastern Asia. Our results highlight the importance of population genomic data and statistical tests in deciphering interspecific relationships and tracing the divergence histories of closely related species.

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Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World's Most Threatened Primates

10.1101/2021.04.16.440058 ◽

2021 ◽

Author(s):

Joanna Malukiewicz ◽

Reed Austin Cartwright ◽

Jorge A Dergam ◽

Claudia S Igayara ◽

Patricia A Nicola ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Data ◽

Nanopore Sequencing ◽

Model Species ◽

Direct Dna Sequencing ◽

Technical Requirements ◽

Exotic Invasive ◽

Complete Mitogenome ◽

Diversity Estimates ◽

Callithrix Aurita

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

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Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

Frontiers in Plant Science ◽

10.3389/fpls.2021.645735 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mi-Jeong Yoo ◽

Byoung-Yoon Lee ◽

Sangtae Kim ◽

Chae Eun Lim

Keyword(s):

Phylogenetic Analyses ◽

Ornamental Plants ◽

Introgressive Hybridization ◽

Nuclear Gene ◽

Genomic Data ◽

Data Set ◽

History Of ◽

Large Genome Size ◽

Taxonomic Confusion ◽

Do So

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

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Assessing Pathogens for Natural versus Laboratory Origins Using Genomic Data and Machine Learning

10.1101/079541 ◽

2016 ◽

Author(s):

Tonia Korves ◽

Christopher Garay ◽

Heather A. Carleton ◽

Ashley Sabol ◽

Eija Trees ◽

...

Keyword(s):

Machine Learning ◽

Large Scale ◽

Phylogenetic Analyses ◽

Bacterial Pathogen ◽

Genomic Data ◽

Ancestral State ◽

Analysis Methods ◽

Laboratory Reference ◽

Serovar Typhimurium ◽

Laboratory Culturing

AbstractPathogen genomic data is increasingly important in investigations of infectious disease outbreaks. The objective of this study is to develop methods for using large-scale genomic data to determine the type of the environment an outbreak pathogen came from. Specifically, this study focuses on assessing whether an outbreak strain came from a natural environment or experienced substantial laboratory culturing. The approach uses phylogenetic analyses and machine learning to identify DNA changes that are characteristic of laboratory culturing. The analysis methods include parallelized sequence read alignment, variant identification, phylogenetic tree construction, ancestral state reconstruction, semi-supervised classification, and random forests. These methods were applied to 902 Salmonella enterica serovar Typhimurium genomes from the NCBI Sequence Read Archive database. The analyses identified candidate signatures of laboratory culturing that are highly consistent with genes identified in published laboratory passage studies. In particular, the analysis identified mutations in rpoS, hfq, rfb genes, acrB, and rbsR as strong signatures of laboratory culturing. In leave-one-out cross-validation, the classifier had an area under the receiver operating characteristic (ROC) curve of 0.89 for strains from two laboratory reference sets collected in the 1940’s and 1980’s. The classifier was also used to assess laboratory culturing in foodborne and laboratory acquired outbreak strains closely related to laboratory reference strain serovar Typhimurium 14028. The classifier detected some evidence of laboratory culturing on the phylogeny branch leading to this clade, suggesting all of these strains may have a common ancestor that experienced laboratory culturing. Together, these results suggest that phylogenetic analysis and machine learning could be used to assess whether pathogens collected from patients are naturally occurring or have been extensively cultured in laboratories. The data analysis methods can be applied to any bacterial pathogen species, and could be adapted to assess viral pathogens and other types of source environments.

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Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution

10.1101/2021.01.12.426373 ◽

2021 ◽

Cited By ~ 1

Author(s):

B. Vrancken ◽

S. Dellicour ◽

D.M. Smith ◽

A Chaillon

Keyword(s):

Convergent Evolution ◽

Phylogenetic Analyses ◽

Genomic Data ◽

Unique Contribution ◽

Single Origin

DisclaimerThe authors have withdrawn this manuscript because it will need to be fully actualized to properly acknowledge the contribution of several genomic data contributors, including the unique contribution of the COG-UK consortium. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors

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Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress

PeerJ ◽

10.7717/peerj.6741 ◽

2019 ◽

Vol 7 ◽

pp. e6741 ◽

Cited By ~ 2

Author(s):

He Li ◽

Xiaojiao Han ◽

Wenmin Qiu ◽

Dong Xu ◽

Ying Wang ◽

...

Keyword(s):

Heavy Metal ◽

Phylogenetic Analyses ◽

Family Members ◽

Genomic Data ◽

Stress Conditions ◽

Metal Exposure ◽

Cd Stress ◽

Hub Genes ◽

Sequence Alignments ◽

Cd Tolerance

Background The herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family’s responses to heavy metal-stress conditions. Methods Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd. Results We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed. Conclusion Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved domain, motif and expression profiling of the GELP family under Cd-stress conditions. SaGLIP8 could increase Cd tolerance and accumulation in yeast. These results indicated the roles of GELPs in plant responses to heavy metal exposure and provides a theoretical basis for further studies of the SaGELP family’s functions.

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Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Scientific Reports ◽

10.1038/s41598-021-96404-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Joanna Malukiewicz ◽

Reed A. Cartwright ◽

Jorge A. Dergam ◽

Claudia S. Igayara ◽

Patricia A. Nicola ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Data ◽

Nanopore Sequencing ◽

Model Species ◽

Direct Dna Sequencing ◽

Technical Requirements ◽

Exotic Invasive ◽

Complete Mitogenome ◽

Diversity Estimates ◽

Callithrix Aurita

AbstractThe Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

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A guide to phylotranscriptomic analysis for phycologists

ALGAE ◽

10.4490/algae.2021.36.12.7 ◽

2021 ◽

Vol 36 (4) ◽

pp. 333-340

Author(s):

Seongmin Cheon ◽

Sung-Gwon Lee ◽

Hyun-Hee Hong ◽

Hyun-Gwan Lee ◽

Kwang Young Kim ◽

...

Keyword(s):

Dna Sequences ◽

Transcriptome Sequencing ◽

Evolutionary Biology ◽

Low Cost ◽

Phylogenetic Analyses ◽

Genomic Data ◽

Command Line ◽

Command Line Interface ◽

Training And Education ◽

Unix Command

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.

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