Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations

We provide in this study a very large DNA dataset on Rhodnius species including 36 samples representing 16 valid species of the three Rhodnius groups, pictipes, prolixus and pallescens. Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the Rhodnius phylogeny. At the species level, we confirmed the species-specific status of R. montenegrensis and R. marabaensis and we agree with the synonymy of R. taquarussuensis with R. neglectus. We also invite to revisit the species-specific status of R. milesi that is more likely R. nasutus. We proposed to define a robustus species complex that comprises the four close relative species: R. marabaensis, R. montenegrensis, R. prolixus and R. robustus. As Psammolestes tertius was included in the Rhodnius clade, we strongly recommend reclassifying this species as R. tertius. At the Rhodnius group level, molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three Rhodnius groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the prolixus group, involving the related species of the robustus complex but also the pairwise R. nasutus and R. neglectus. A genome wide analysis highlighted an introgression event in the pictipes group between R. stali and R. brethesi and suggested a complex gene flow between the three species of the pallescens group, R. colombiensis, R. pallescens and R. ecuadoriensis. The molecular data supports also a sylvatic distribution of R. prolixus in Brazil (Pará state) and the monophyly of R. robustus. As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.

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Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias

Marine Drugs ◽

10.3390/md17070386 ◽

2019 ◽

Vol 17 (7) ◽

pp. 386 ◽

Cited By ~ 6

Author(s):

Chao Bian ◽

Jia Li ◽

Xueqiang Lin ◽

Xiyang Chen ◽

Yunhai Yi ◽

...

Keyword(s):

Genome Assembly ◽

Genetic Resource ◽

Draft Genome ◽

Close Relative ◽

Protein Coding ◽

Oreochromis Aureus ◽

Genome Wide ◽

A Genome ◽

Blue Tilapia ◽

First Time

Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.

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A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle

Genes ◽

10.3390/genes12050643 ◽

2021 ◽

Vol 12 (5) ◽

pp. 643

Author(s):

Thibaud Kuca ◽

Brandy M. Marron ◽

Joana G. P. Jacinto ◽

Julia M. Paris ◽

Christian Gerspach ◽

...

Keyword(s):

Genome Wide Association Study ◽

Homozygosity Mapping ◽

Mendelian Inheritance ◽

Large Animal Model ◽

Large Animal ◽

Loss Of Function ◽

Protein Coding ◽

Positional Candidate ◽

Genome Wide ◽

A Genome

Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).

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The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874)

Zootaxa ◽

10.11646/zootaxa.4512.1.1 ◽

2018 ◽

Vol 4512 (1) ◽

pp. 1

Author(s):

CHRISTINE M. KAISER ◽

HINRICH KAISER ◽

MARK O’SHEA

Keyword(s):

New Guinea ◽

Molecular Data ◽

The Philippines ◽

Morphological Data ◽

Valid Species ◽

Museum Specimens ◽

Type Specimens ◽

History Of ◽

Original Species ◽

Species Specific

Since its conceptualization in 1854, 29 species of the colubrid genus Stegonotus have been recognized or described, of which 15 (admiraltiensis, batjanensis, borneensis, cucullatus, derooijae, diehli, florensis, guentheri, iridis, heterurus, melanolabiatus, modestus, muelleri, parvus, poechi) are still considered valid today. Original species descriptions for the members of this genus were published in Dutch, English, French, German, and Italian and, perhaps as a consequence of these polyglot origins, there has been a considerable amount of confusion over which species names should be applied to which populations of Stegonotus throughout its range across Borneo, the Philippines, Wallacea, New Guinea, Australia, and associated archipelagos. In addition, the terminology used to notate characteristics in the descriptions of these forms was not uniform and may have added to the taxonomic confusion. In this paper, we trace in detail the history of the type specimens, the species, and the synonyms currently associated with the genus Stegonotus and provide a basic, species-specific listing of their characteristics, derived from our examination of over 1500 museum specimens. Based on our data, we are able to limit the distribution of S. modestus to the islands of Ambon, Buru, and Seram in the central Moluccas of Indonesian Wallacea. We correct the type locality of S. cucullatus to the Manokwari area on the Bird’s Head Peninsula of West Papua, Indonesian New Guinea and designate a neotype for S. parvus, a species likely to be a regional endemic in the Schouten Archipelago of Cenderawasih Bay (formerly Geelvink Bay), Indonesian New Guinea. We unequivocally identify and explain the problematic localities of the type specimens of S. muelleri and Lycodon muelleri, which currently reside in the same specimen jar. We remove L. aruensis and L. lividum from the synonymy of S. modestus and recognize them as S. aruensis n. comb. and S. lividus n. comb., respectively. We remove S. keyensis and Zamenophis australis from the synonymy of S. cucullatus and recognize them as S. keyensis n. comb. and S. australis n. comb., respectively. We further remove S. reticulatus from the synonymy of S. cucullatus, S. dorsalis from the synonymy of S. diehli, and S. sutteri from the synonymy of S. florensis. We designate lectotypes for S. guentheri, S. heterurus, S. lividus, and S. reticulatus. Lastly, we introduce S. poechi, a valid species not mentioned in the scientific literature since its description in 1924. This brings the diversity in the genus Stegonotus to 22 species. We also caution that in a complex group of organisms like Stegonotus any rush to taxonomic judgment on the basis of molecular and incomplete morphological data sets may perpetuate errors and introduce incongruities. Only through the careful work of connecting type material with museum specimens and molecular data can the taxonomy and nomenclature of complex taxa be stabilized.

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A porcine brain-wide RNA editing landscape

10.21203/rs.3.rs-110949/v1 ◽

2020 ◽

Author(s):

Jinrong Huang ◽

Lin Lin ◽

Zhanying Dong ◽

Ling Yang ◽

Tianyu Zheng ◽

...

Keyword(s):

Rna Editing ◽

Repetitive Sequences ◽

Brain Regions ◽

Mammalian Brain ◽

Protein Coding ◽

Porcine Brain ◽

Coding Regions ◽

Pig Brain ◽

Genome Wide ◽

A Genome

Abstract Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modiﬁcation. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. The porcine brain-wide RNA landscape provides a rich resource to better understand the evolutionally importance of post-transcriptional RNA editing.

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Selected mitochondrial genes as species markers of the Arctic Contracaecum osculatum complex

Journal of Helminthology ◽

10.1017/s0022149x11000332 ◽

2011 ◽

Vol 86 (2) ◽

pp. 252-258 ◽

Cited By ~ 5

Author(s):

J. Dzido ◽

A. Kijewska ◽

J. Rokicki

Keyword(s):

Barents Sea ◽

Intraspecific Variability ◽

Mitochondrial Genes ◽

Intraspecific Diversity ◽

The Arctic ◽

Protein Coding ◽

As Species ◽

Contracaecum Osculatum ◽

Species Markers ◽

Species Specific

AbstractThis study, aimed at testing the hypothesis that some mitochondrial genes can serve as species-specific markers, involved a comparison of the sequence variance of selected mitochondrial DNA genes of the Arctic Contracaecum osculatum species (C. osculatum A, C. osculatum B and C. osculatum C). We compared differences between five complete (ND2, CYTB, ND3, ND4L and ND6) and three partial (CO1, CO3 and ND5) protein-coding genes. The total length of the sequence of each of the 13 specimens was 4830 bp. The sample consisted of C. osculatum L3 larvae collected from Reinhardtius hippoglossoides and Gadus ogac from the Barents Sea and Davis Strait. The K2P distance values between the species ranged within 0.06–0.12, the intraspecific variability (0.01–0.03) proving 3–6 times lower. The lowest interspecific divergence was observed between C. osculatum A and C. osculatum B, whereas the highest intraspecific diversity was typical of C. osculatum C. Among the C. osculatum species studied, the highest nucleotide diversity was recorded in the CYTB, CO3 and ND5 genes. These genes may be useful in species identification of the very closely related Contracaecum sibling species.

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Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

10.1101/2021.08.09.455628 ◽

2021 ◽

Author(s):

Raz Avni ◽

Thomas Lux ◽

Anna Minz-Dub ◽

Eitan Millet ◽

Hanan Sela ◽

...

Keyword(s):

Haplotype Block ◽

Close Relative ◽

Whole Genome ◽

Aegilops Species ◽

Wheat Improvement ◽

Genome Wide ◽

Triticum Spp ◽

Species Specific ◽

Genomic Regions ◽

Genome Assemblies

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly simiar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

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Host cell factors important for BHV-1 cell entry revealed by genome-wide CRISPR knockout screen

10.1101/2020.06.18.160523 ◽

2020 ◽

Author(s):

Wenfang Spring Tan ◽

Enguang Rong ◽

Inga Dry ◽

Simon Lillico ◽

Andy Law ◽

...

Keyword(s):

Host Cell ◽

Viral Entry ◽

Surface Proteins ◽

Chain Elongation ◽

Related Factors ◽

Protein Coding ◽

Cog Complex ◽

Genome Wide ◽

A Genome ◽

Mdbk Cells

AbstractIn order to identify host factors that impact Bovine Herpes Virus Type 1 (BHV-1) infection we previously applied a genome wide CRISPR knockout screen with a library covering all bovine protein coding genes. We compiled a list of both pro-viral and anti-viral proteins involved in BHV-1 replication; here we provide further analysis of those that are potentially involved in viral entry into the host cell. These entry related factors include the cell surface proteins PVR and PVRL2, a group of enzymes directly or indirectly associated with the biosynthesis of Heparan Sulfate Proteoglycans (HSPG), and proteins that reside in the Golgi apparatus engaging in intra-Golgi trafficking. For the first time, we provide evidence that PVRL2 serves a receptor for BHV-1, mediating more efficient entry than the previously identified PVR. By knocking out two enzymes that catalyze HSPG chain elongation, HST2ST1 and GLCE, we demonstrated the significance of HSPG in BHV-1 entry. Another intriguing cluster of genes, COG1, COG2 and COG4-7 encodes for six subunits of the conserved oligomeric Golgi (COG) complex. MDBK cells lacking COG6 were less infectable by BHV-1 but release newly produced virions more efficiently as evidenced by fewer but bigger plaques compared to control cells, suggesting impaired HSPG biosynthesis. To facilitate candidate validation, we devised a one-step multiplex CRISPR interference (CRISPRi) system named CRISPR3i that enables quick and simultaneous deployment of three CRISPRs for efficient gene inactivation. Using CRISPR3i, we verified an additional 23 candidates, with many implicated in cellular entry.

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Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly

10.1101/117176 ◽

2017 ◽

Cited By ~ 1

Author(s):

Filip Ruzicka ◽

Mark S. Hill ◽

Tanya M. Pennell ◽

Ilona Flis ◽

Fiona C. Ingleby ◽

...

Keyword(s):

Sexual Dimorphism ◽

Evolutionary Dynamics ◽

Genome Wide Association Study ◽

Balancing Selection ◽

Sexual Antagonism ◽

Protein Coding ◽

Genome Wide ◽

Genomic Location ◽

Classic Theory ◽

A Genome

The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’ where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

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Genome-Wide Transcriptional Changes in Streptococcus gordonii in Response to Competence Signaling Peptide

Journal of Bacteriology ◽

10.1128/jb.01023-07 ◽

2007 ◽

Vol 189 (21) ◽

pp. 7799-7807 ◽

Cited By ~ 76

Author(s):

M. M. Vickerman ◽

S. Iobst ◽

A. M. Jesionowski ◽

S. R. Gill

Keyword(s):

Transcriptional Response ◽

Streptococcus Gordonii ◽

Direct Repeats ◽

Multispecies Biofilm ◽

Genome Wide ◽

A Genome ◽

Tooth Surfaces ◽

Transcriptional Changes ◽

Species Specific ◽

Regulatory Sites

ABSTRACT Streptococcus gordonii is a primary colonizer of the multispecies biofilm on tooth surfaces forming dental plaque and a potential agent of endocarditis. The recent completion of the genome sequence of the naturally competent strain Challis allowed the design of a spotted oligonucleotide microarray to examine a genome-wide response of this organism to environmental stimuli such as signal peptides. Based on temporal responses to synthetic competence signaling peptide (CSP) as indicated by transformation frequencies, the S. gordonii transcriptome was analyzed at various time points after CSP exposure. Microarray analysis identified 35 candidate early genes and 127 candidate late genes that were up-regulated at 5 and 15 min, respectively; these genes were often grouped in clusters. Results supported published findings on S. gordonii competence, showing up-regulation of 12 of 16 genes that have been reported to affect transformation frequencies in this species. Comparison of CSP-induced S. gordonii transcriptomes to results published for Streptococcus pneumoniae strains identified both conserved and species-specific genes. Putative intergenic regulatory sites, such as the conserved combox sequence thought to be a binding site for competence sigma factor, were found preceding S. gordonii late responsive genes. In contrast, S. gordonii early CSP-responsive genes were not preceded by the direct repeats found in S. pneumoniae. These studies provide the first insights into a genome-wide transcriptional response of an oral commensal organism. They offer an extensive analysis of transcriptional changes that accompany competence in S. gordonii and form a basis for future intra- and interspecies comparative analyses of this ecologically important phenotype.

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Genotypic variation of gene expression during the soybean innate immunity response

Plant Genetic Resources ◽

10.1017/s1479262114000197 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S27-S30 ◽

Cited By ~ 3

Author(s):

Oswaldo Valdés-López ◽

Saad M. Khan ◽

Robert J. Schmitz ◽

Shiqi Cui ◽

Jing Qiu ◽

...

Keyword(s):

Gene Expression ◽

Innate Immunity ◽

Plant Species ◽

Genotypic Variation ◽

Additive Effects ◽

Molecular Pattern ◽

Genome Wide ◽

A Genome ◽

Immunity Response ◽

Species Specific

Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. Although several MTI responses can be measured in different plant species, their magnitude is probably plant species specific and even cultivar specific. In this study, a genome-wide transcriptome analysis of two soybean parental lines and two progeny lines treated for 30 min with the MAMPs flg22 and chitin was carried out. This analysis revealed a clear variation in gene expression, under both untreated and flg22+chitin-treated conditions. In addition, genes with potential additive and non-additive effects were identified in the two progeny lines, with several of these genes having a potential function in the control of innate immunity. The data presented herein represent the basis for further functional analysis that can lead to a better understanding of the soybean innate immunity response.

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