Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

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Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423790112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10200-10207 ◽

Cited By ~ 117

Author(s):

Jan Janouškovec ◽

Denis V. Tikhonenkov ◽

Fabien Burki ◽

Alexis T. Howe ◽

Martin Kolísko ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Sister Group ◽

Molecular Characteristics ◽

Phylogenomic Analysis ◽

Free Living ◽

Plastid Genomes ◽

Monophyletic Lineage ◽

Causative Agents ◽

Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

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Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

Systematic Biology ◽

10.1093/sysbio/syaa075 ◽

2020 ◽

Cited By ~ 1

Author(s):

Robert S de Moya ◽

Kazunori Yoshizawa ◽

Kimberly K O Walden ◽

Andrew D Sweet ◽

Christopher H Dietrich ◽

...

Keyword(s):

Sequence Data ◽

Compositional Bias ◽

Phylogenomic Analysis ◽

Data Set ◽

Genomic Changes ◽

Insect Order ◽

Codon Positions ◽

Phylogenomic Analyses ◽

Ordinal Level ◽

Likelihood Mapping

Abstract The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

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Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000226 ◽

2015 ◽

Vol 65 (Pt_7) ◽

pp. 2104-2109 ◽

Cited By ~ 48

Author(s):

Christopher A. Dunlap ◽

Soo-Jin Kim ◽

Soon-Wo Kwon ◽

Alejandro P. Rooney

Keyword(s):

Bacillus Amyloliquefaciens ◽

Type Strain ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Growth Promoters ◽

Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

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Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)

PeerJ ◽

10.7717/peerj.6959 ◽

2019 ◽

Vol 7 ◽

pp. e6959 ◽

Cited By ~ 7

Author(s):

Lauren M. Orton ◽

Sean V. Burke ◽

Melvin R. Duvall

Keyword(s):

Strong Support ◽

Data Matrix ◽

Phylogenomic Analysis ◽

Genomic Change ◽

Genomic Changes ◽

Plastid Genomes ◽

Rare Genomic Changes ◽

Group 2 ◽

Taxonomic Markers ◽

Group 1

A phylogenomic analysis of 42 complete plastid genomes (plastomes), including 16 that were newly sequenced, was conducted. Plastomes were sampled from 19 subtribes of Pooideae, to investigate relationships within and between Chloroplast Group 1 (Aveneae) and Group 2 (Poeae) species. Two data partitions: complete plastomes, and a combined plastome and rare genomic change (RGC) data matrix, were analyzed. Overall, 156 non-ambiguous RGC were identified, of which homology was inferred for 38 RGC. Among the 38 RGC identified, six were synapomorphic among the Group 1 subtribes: Aveninae, Agrostidinae, and Anthoxanthinae, (Phalaridinae + Torreyochloinae), and 27 were synapomorphic among the Group 2 subtribes: Loliinae, (Ammochloinae + Parapholiinae + Dactylidinae), Parapholiinae, Dactylidinae, Poinae, and Coleanthinae. Four RGC were determined to be homoplasious in Groups 1 and 2. Two other RGC originated through intrastrand deletion events. The remaining RGC events likely originated through recombination given their size and lack of sequence evidence for other types of mutations. This study also determined that relationships between taxa, even those only weakly supported in previous studies, could be inferred with strong support when utilizing complete plastomes.

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Mitochondrial Genomes Provide Insights into the Phylogeny of Culicomorpha (Insecta: Diptera)

International Journal of Molecular Sciences ◽

10.3390/ijms20030747 ◽

2019 ◽

Vol 20 (3) ◽

pp. 747 ◽

Cited By ~ 2

Author(s):

Xiao Zhang ◽

Zehui Kang ◽

Shuangmei Ding ◽

Yuyu Wang ◽

Chris Borkent ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Sister Group ◽

Monophyletic Group ◽

Phylogenomic Analysis ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Genome Data ◽

New Family ◽

Mt Genome

Culicomorpha is a monophyletic group containing most bloodsucking lower dipterans, including many important vectors of pathogens. However, the higher-level phylogenetic relationships within Culicomorpha are largely unresolved, with multiple competing hypotheses based on molecular sequence data. Here we sequenced four nearly complete mitochondrial (mt) genomes representing four culicomorph families, and combined these new data with published mt genomes to reconstruct the phylogenetic relationships of all eight extant culicomorph families. We estimated phylogenies using four datasets and three methods. We also used four-cluster likelihood mapping to study potential incongruent topologies supported by the different datasets and phylogenetic questions generated by the previous studies. The results showed that a clade containing Ceratopogonidae, Thaumaleidae and Simuliidae was the sister group to all other Culicomorpha; in another clade, the Dixidae was basal to the remaining four families; Chaoboridae, Corethrellidae and Culicidae formed a monophyletic group and the Chironomidae was the sister group to this clade; Culicidae and Corethrellidae were sister groups in all trees. Our study provides novel mt genome data in Culicomorpha for three new family representatives, and the resulting mt phylogenomic analysis helps to resolve the phylogeny and taxonomy of Culicomorpha.

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Genomic Changes during Chronic Helicobacter pylori Infection

Journal of Bacteriology ◽

10.1128/jb.188.1.249-254.2006 ◽

2006 ◽

Vol 188 (1) ◽

pp. 249-254 ◽

Cited By ~ 58

Author(s):

Christian Kraft ◽

Allison Stack ◽

Christine Josenhans ◽

Eike Niehus ◽

Guido Dietrich ◽

...

Keyword(s):

Helicobacter Pylori ◽

Dna Microarrays ◽

Sequence Data ◽

Great Majority ◽

Human Populations ◽

Genetic Changes ◽

Genomic Change ◽

Genomic Changes ◽

Genome Content ◽

H Pylori

ABSTRACT The gastric pathogen Helicobacter pylori shows tremendous genetic variability within human populations, both in gene content and at the sequence level. We investigated how this variability arises by comparing the genome content of 21 closely related pairs of isolates taken from the same patient at different time points. The comparisons were performed by hybridization with whole-genome DNA microarrays. All loci where microarrays indicated a genomic change were sequenced to confirm the events. The number of genomic changes was compared to the number of homologous replacement events without loss or gain of genes that we had previously determined by multilocus sequence analysis and mathematical modeling based on the sequence data. Our analysis showed that the great majority of genetic changes were due to homologous recombination, with 1/650 events leading to a net gain or loss of genes. These results suggest that adaptation of H. pylori to the host individual may principally occur through sequence changes rather than loss or gain of genes.

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Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.000444 ◽

2015 ◽

Vol 65 (Pt_10) ◽

pp. 3507-3510 ◽

Cited By ~ 16

Author(s):

Christopher A. Dunlap

Keyword(s):

Dna Hybridization ◽

Core Genome ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Sequencing Analysis ◽

Emended Description ◽

Type Strains

‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

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Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its “Jekyll and Hyde” Mode of Infection Pattern

Genome Biology and Evolution ◽

10.1093/gbe/evaa006 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3818-3831 ◽

Cited By ~ 6

Author(s):

Xiao-Li Bing ◽

Dian-Shu Zhao ◽

Jing-Tao Sun ◽

Kai-Jun Zhang ◽

Xiao-Yue Hong

Keyword(s):

Draft Genome ◽

Genomic Analysis ◽

Phylogenomic Analysis ◽

Laodelphax Striatellus ◽

Secretion Systems ◽

Negative Effects ◽

Protein Coding ◽

Catalytic Domains ◽

Infection Pattern ◽

Wolbachia Genome

Abstract Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a “Jekyll and Hyde” mode of infection pattern with positive and negative effects: It not only kills many offspring by inducing cytoplasmic incompatibility (CI) but also significantly increases host fecundity. In this study, we assembled the draft genome of wStriCN and compared it with other Wolbachia genomes to look for clues to its Jekyll and Hyde characteristics. The assembled wStriCN draft genome is 1.79 Mb in size, which is the largest Wolbachia genome in supergroup B. Phylogenomic analysis showed that wStriCN is closest to Wolbachia from Asian citrus psyllid Diaphorina citri. These strains formed a monophylogentic clade within supergroup B. Compared with other Wolbachia genomes, wStriCN contains the most diverse insertion sequence families, the largest amount of prophage sequences, and the most ankyrin domain protein coding genes. The wStriCN genome encodes components of multiple secretion systems, including Types I, II, IV, VI, Sec, and Tac. We detected three pairs of homologs for CI factors CifA and CifB. These proteins harbor the catalytic domains responsible for CI phenotypes but are phylogenetically and structurally distinct from all known Cif proteins. The genome retains pathways for synthesizing biotin and riboflavin, which may explain the beneficial roles of wStriCN in its host planthoppers, which feed on nutrient-poor plant sap. Altogether, the genomic sequencing of wStriCN provides insight into understanding the phylogeny and biology of Wolbachia.

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What Have We Learned from the First 500 Avian Genomes?

Annual Review of Ecology Evolution and Systematics ◽

10.1146/annurev-ecolsys-012121-085928 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Gustavo A. Bravo ◽

C. Jonathan Schmitt ◽

Scott V. Edwards

Keyword(s):

Population Genomics ◽

Sequence Data ◽

Genome Project ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Bird Diversity ◽

Annual Review ◽

Publication Date ◽

Genomic Changes ◽

Rare Genomic Changes

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab019 ◽

2021 ◽

Vol 11 (2) ◽

Author(s):

Gherard Batisti Biffignandi ◽

Marjorie J Gibbon ◽

Marta Corbella ◽

Harry A Thorpe ◽

Cristina Merla ◽

...

Keyword(s):

New Species ◽

Draft Genome ◽

Gc Content ◽

Sister Group ◽

Sister Group Relationship ◽

Phylogenomic Analysis ◽

The Novel ◽

Antimicrobial Resistance Genes ◽

The Family ◽

A New Species

Abstract During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”

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