scholarly journals Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 385 ◽  
Author(s):  
Rebekkah J. Hitti ◽  
James A. C. Oliver ◽  
Ellen C. Schofield ◽  
Anina Bauer ◽  
Maria Kaukonen ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Whole Genome Sequencing ◽  
Retinal Degeneration ◽  
Genome Sequencing ◽  
Autosomal Recessive Disorder ◽  
Causal Variant ◽  
Whole Genome ◽  
Gene Encoding ◽  
Progressive Retinal Atrophy ◽  
Dna Test

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.

scholarly journals Homburgvirus LP-018 Has a Unique Ability to Infect Phage-Resistant Listeria monocytogenes

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1166 ◽  
Author(s):  
Yaxiong Song ◽  
Tracey L. Peters ◽  
Daniel W. Bryan ◽  
Lauren K. Hudson ◽  
Thomas G. Denes
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Burst Size ◽  
Resistant Mutant ◽  
Whole Genome ◽  
Single Mutation ◽  
Growth Curve Analysis ◽  
Gene Encoding ◽  
Phage Resistant Mutant

Listeria phage LP-018 is the only phage from a diverse collection of 120 phages able to form plaques on a phage-resistant Listeria monocytogenes strain lacking rhamnose in its cell wall teichoic acids. The aim of this study was to characterize phage LP-018 and to identify what types of mutations can confer resistance to LP-018. Whole genome sequencing and transmission electron microscopy revealed LP-018 to be a member of the Homburgvirus genus. One-step-growth curve analysis of LP-018 revealed an eclipse period of ~60–90 min and a burst size of ~2 PFU per infected cell. Despite slow growth and small burst size, LP-018 can inhibit the growth of Listeria monocytogenes at a high multiplicity of infection. Ten distinct LP-018-resistant mutants were isolated from infected Listeria monocytogenes 10403S and characterized by whole genome sequencing. In each mutant, a single mutation was identified in either the LMRG_00278 or LMRG_01613 encoding genes. Interesting, LP-018 was able to bind to a representative phage-resistant mutant with a mutation in each gene, suggesting these mutations confer resistance through a mechanism independent of adsorption inhibition. Despite forming plaques on the rhamnose deficient 10403S mutant, LP-018 showed reduced binding efficiency, and we did not observe inhibition of the strain under the conditions tested. Two mutants of LP-018 were also isolated and characterized, one with a single SNP in a gene encoding a BppU domain protein that likely alters its host range. LP-018 is shown to be a unique Listeria phage that, with additional evaluation, may be useful in biocontrol applications that aim to reduce the emergence of phage resistance.

scholarly journals A Missense Mutation in the KLF7 Gene Is a Potential Candidate Variant for Congenital Deafness in Australian Stumpy Tail Cattle Dogs

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 467
Author(s):  
Fangzheng Xu ◽  
Shuwen Shan ◽  
Susan Sommerlad ◽  
Jennifer M. Seddon ◽  
Bertram Brenig
Keyword(s):  
Candidate Gene ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Heart Development ◽  
Genome Wide Association Study ◽  
Whole Genome ◽  
Potential Candidate ◽  
Congenital Deafness ◽  
Cardiovascular Development ◽  
A Genome

Congenital deafness is prevalent among modern dog breeds, including Australian Stumpy Tail Cattle Dogs (ASCD). However, in ASCD, no causative gene has been identified so far. Therefore, we performed a genome-wide association study (GWAS) and whole genome sequencing (WGS) of affected and normal individuals. For GWAS, 3 bilateral deaf ASCDs, 43 herding dogs, and one unaffected ASCD were used, resulting in 13 significantly associated loci on 6 chromosomes, i.e., CFA3, 8, 17, 23, 28, and 37. CFA37 harbored a region with the most significant association (−log10(9.54 × 10−21) = 20.02) as well as 7 of the 13 associated loci. For whole genome sequencing, the same three affected ASCDs and one unaffected ASCD were used. The WGS data were compared with 722 canine controls and filtered for protein coding and non-synonymous variants, resulting in four missense variants present only in the affected dogs. Using effect prediction tools, two variants remained with predicted deleterious effects within the Heart development protein with EGF like domains 1 (HEG1) gene (NC_006615.3: g.28028412G>C; XP_022269716.1: p.His531Asp) and Kruppel-like factor 7 (KLF7) gene (NC_006619.3: g.15562684G>A; XP_022270984.1: p.Leu173Phe). Due to its function as a regulator in heart and vessel formation and cardiovascular development, HEG1 was excluded as a candidate gene. On the other hand, KLF7 plays a crucial role in the nervous system, is expressed in the otic placode, and is reported to be involved in inner ear development. 55 additional ASCD samples (28 deaf and 27 normal hearing dogs) were genotyped for the KLF7 variant, and the variant remained significantly associated with deafness in ASCD (p = 0.014). Furthermore, 24 dogs with heterozygous or homozygous mutations were detected, including 18 deaf dogs. The penetrance was calculated to be 0.75, which is in agreement with previous reports. In conclusion, KLF7 is a promising candidate gene causative for ASCD deafness.

scholarly journals An Alu-mediated duplication in NMNAT1, involved in NAD biosynthesis, causes a novel syndrome, SHILCA, affecting multiple tissues and organs

2020 ◽  
Vol 29 (13) ◽  
pp. 2250-2260 ◽  
Author(s):  
Nicola Bedoni ◽  
Mathieu Quinodoz ◽  
Michele Pinelli ◽  
Gerarda Cappuccio ◽  
Annalaura Torella ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Autosomal Recessive Disorder ◽  
Severe Form ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Leber Congenital Amaurosis ◽  
Pathogenic Variants ◽  
Long Read ◽  
Biallelic Mutations

Abstract We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients’ fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.

scholarly journals Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree

Genes ◽  
2017 ◽  
Vol 8 (9) ◽  
pp. 210 ◽  
Author(s):  
Kevin Gustafson ◽  
Jacque Duncan ◽  
Pooja Biswas ◽  
Angel Soto-Hermida ◽  
Hiroko Matsui ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Retinal Degeneration ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Ashkenazi Jewish

scholarly journals Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants

2021 ◽  
Vol 12 ◽  
Author(s):  
Hanna Marti ◽  
Sankhya Bommana ◽  
Timothy D. Read ◽  
Theresa Pesch ◽  
Barbara Prähauser ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Homologous Recombination ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Field Isolate ◽  
Tetracycline Resistance ◽  
Whole Genome ◽  
Gene Encoding ◽  
Obligate Intracellular

The Chlamydiaceae are a family of obligate intracellular, gram-negative bacteria known to readily exchange DNA by homologous recombination upon co-culture in vitro, allowing the transfer of antibiotic resistance residing on the chlamydial chromosome. Among all the obligate intracellular bacteria, only Chlamydia (C.) suis naturally integrated a tetracycline resistance gene into its chromosome. Therefore, in order to further investigate the readiness of Chlamydia to exchange DNA and especially antibiotic resistance, C. suis is an excellent model to advance existing co-culture protocols allowing the identification of factors crucial to promote homologous recombination in vitro. With this strategy, we co-cultured tetracycline-resistant with rifamycin group-resistant C. suis, which resulted in an allover recombination efficiency of 28%. We found that simultaneous selection is crucial to increase the number of recombinants, that sub-inhibitory concentrations of tetracycline inhibit rather than promote the selection of double-resistant recombinants, and identified a recombination-deficient C. suis field isolate, strain SWA-110 (1-28b). While tetracycline resistance was detected in field isolates, rifampicin/rifamycin resistance (RifR) had to be induced in vitro. Here, we describe the protocol with which RifR C. suis strains were generated and confirmed. Subsequent whole-genome sequencing then revealed that G530E and D461A mutations in rpoB, a gene encoding for the β-subunit of the bacterial RNA polymerase (RNAP), was likely responsible for rifampicin and rifamycin resistance, respectively. Finally, whole-genome sequencing of recombinants obtained by co-culture revealed that recombinants picked from the same plate may be sibling clones and confirmed C. suis genome plasticity by revealing variable, apparently non-specific areas of recombination.

scholarly journals Detection of Candidate Gene LsACOS5 and Development of InDel Marker for Male Sterility by DdRAD-Seq and Whole-Genome Sequencing in Lettuce (Lactuca Sativa L.)

2021 ◽  
Author(s):  
kousuke seki
Keyword(s):  
Candidate Gene ◽  
Whole Genome Sequencing ◽  
Male Sterility ◽  
Genome Sequencing ◽  
Indel Marker ◽  
Hybrid Breeding ◽  
Whole Genome ◽  
Structural Polymorphism ◽  
Male Sterile ◽  
Breeding Method

Abstract A new breeding method of F1 hybrid using male sterility would open an exciting frontier in lettuce breeding, a self-pollinating crop. Male sterility is a crucial trait in F1 hybrid breeding. It is essential to map the causative gene for using male sterility. The ms-S, male-sterile gene of ‘CGN17397’, was mapped to LG8 by double-digest restriction site-associated DNA sequencing (ddRAD-seq) and narrowed down between two markers using two F2 populations. This region spans approximately 10.16 Mb, where 94 genes were annotated according to the lettuce reference genome sequence (version8 from crisphead cultivar ‘Salinas’). The whole-genome sequencing of the male-sterile and fertile lines of ‘CGN17397’ revealed that only one gene differed in the area of Lsat_1_v5_gn_8_148221.1, a homolog of Arabidopsis acyl-CoA synthetase5 (AtACOS5), and was deleted in the male-sterile lines. It was reported that AtACOS5 was needed for pollen wall formation and that the null mutants of AtACOS5 were entirely male sterility. Thus, I concluded that Lsat_1_v5_gn_8_148221.1 designated as LsACOS5 was a biologically plausible candidate gene for the ms-S locus. By using the structural polymorphism of LsACOS5, an insertion/deletion (InDel) marker was developed to select the male-sterile trait. The results obtained here provide valuable information for the genic male-sterility in lettuce.

scholarly journals Emergence of Carbapenem-Resistant Pseudomonas asiatica Producing NDM-1 and VIM-2 Metallo-β-Lactamases in Myanmar

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
Mari Tohya ◽  
Tatsuya Tada ◽  
Shin Watanabe ◽  
Kyoko Kuwahara-Arai ◽  
Khwar Nyo Zin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Gene Encoding ◽  
Medical Settings ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
16S Rrna Methylase

ABSTRACT Pseudomonas asiatica is a recently proposed species of the genus Pseudomonas. This study describes eight isolates of carbapenem-resistant P. asiatica harboring blaNDM-1 and blaVIM-2, genes encoding metallo-β-lactamase (MBL). These isolates were obtained from urine samples of patients hospitalized in Myanmar. These isolates were resistant to carbapenems but susceptible to colistin. All eight isolates were positive for a carbapenemase inactivation method, CIMTrisII, and seven were positive on an immunochromatographic assay for NDM-type MBL. One isolate was highly resistant to aminoglycosides. Whole-genome sequencing showed that seven isolates harbored blaNDM-1 and one harbored blaVIM-2, with these genes located on the chromosome. One isolate harbored blaNDM-1 and rmtC, a gene encoding 16S rRNA methylase. Five types of genomic environments surrounding blaNDM-1 and blaVIM-2 were detected in these eight isolates, with four isolates having the same type. These data indicate that P. asiatica isolates harboring genes encoding carbapenemases, including blaNDM-1 and blaVIM-2, are spreading in medical settings in Myanmar.

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