scholarly journals Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Israel Guerrero-Cózar ◽  
Jessica Gomez-Garrido ◽  
Concha Berbel ◽  
Juan F. Martinez-Blanch ◽  
Tyler Alioto ◽  
...  
Keyword(s):  
Genetic Map ◽  
De Novo ◽  
Sequence Similarity ◽  
Snp Markers ◽  
Genetic Maps ◽  
Solea Senegalensis ◽  
Incomplete Penetrance ◽  
Senegalese Sole ◽  
High Sequence Similarity ◽  
Chromosome Level

AbstractThe integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.

scholarly journals Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Israel Guerrero-Cózar ◽  
Cathaysa Perez-Garcia ◽  
Hicham Benzekri ◽  
J. J. Sánchez ◽  
Pedro Seoane ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Map ◽  
De Novo ◽  
Pedigree Analysis ◽  
Solea Senegalensis ◽  
Whole Genome ◽  
Senegalese Sole ◽  
A Genome ◽  
Genome Draft ◽  
Integrated Genetic Map

AbstractThe Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.

scholarly journals Isolation of Cysteine-Rich Peptides from Citrullus colocynthis

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1326
Author(s):  
Behzad Shahin-Kaleybar ◽  
Ali Niazi ◽  
Alireza Afsharifar ◽  
Ghorbanali Nematzadeh ◽  
Reza Yousefi ◽  
...  
Keyword(s):  
Trypsin Inhibitor ◽  
High Performance ◽  
De Novo ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
Reversed Phase ◽  
Amino Acid Sequences ◽  
Peptide Fragments ◽  
Citrullus Colocynthis ◽  
High Sequence Similarity

The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

scholarly journals A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

2021 ◽  
pp. 1-7
Author(s):  
Prashant Bhandari ◽  
Tong Geon Lee
Keyword(s):  
Genetic Map ◽  
Recombination Frequency ◽  
Average Distance ◽  
Genetic Research ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphism ◽  
Fresh Market ◽  
Crop Breeding ◽  
Single Nucleotide

Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.

scholarly journals Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Marianella Quezada ◽  
Rodrigo Rampazo Amadeu ◽  
Beatriz Vignale ◽  
Danilo Cabrera ◽  
Clara Pritsch ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Research ◽  
Diploid Species ◽  
Eucalyptus Grandis ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Acca Sellowiana ◽  
Marker Distance ◽  
Connected Populations

Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858)

2014 ◽  
Vol 17 (1) ◽  
pp. 8-22 ◽  
Author(s):  
Ma. Jesús Molina-Luzón ◽  
Miguel Hermida ◽  
Rafael Navajas-Pérez ◽  
Francisca Robles ◽  
José Ignacio Navas ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genetic Map ◽  
Solea Senegalensis ◽  
Senegalese Sole

De novo assembly and characterisation of the transcriptome of the Beringian pseudoscorpion

2021 ◽  
pp. 1-13
Author(s):  
Jacqueline E. Lebenzon ◽  
Jantina Toxopeus ◽  
Susan E. Anthony ◽  
Brent J. Sinclair
Keyword(s):  
De Novo ◽  
Sequence Similarity ◽  
Arctic Region ◽  
Single Copy ◽  
Yukon Territory ◽  
The Arctic ◽  
Sequence Information ◽  
High Sequence Similarity ◽  
Shock Proteins ◽  
Venom Proteins

Abstract Pseudoscorpions are microarthropods that are distributed from the equator to beyond the Arctic circle. Wyochernes asiaticus (Arachnida: Pseudoscorpiones: Chernetidae) is the northernmost species of pseudoscorpion and is broadly distributed in Beringia, an Arctic and sub-Arctic region that remained unglaciated during the last glacial maximum. Wyochernes asiaticus is anoxia tolerant and has moderate cold tolerance, but nothing is known about the molecular basis of their survival in Canadian polar environments. We de novo assembled and characterised the transcriptome of W. asiaticus collected from the Yukon Territory in northwestern Canada. We assembled an approximately 62.6-million base-pair transcriptome with a mean contig length of 1277, which was 76% complete, according to a benchmark universal single copy orthologue (BUSCO) analysis. We identified 1100 transcripts encoding proteins associated with stress tolerance in these pseudoscorpions, including heat shock proteins, antioxidants, ubiquitination and proteosomal proteins, and sirtuins. We also identified transcripts encoding putative venom proteins. We highlight eight transcripts with high sequence similarity to sequences of venom proteins (ctenitoxins and agatoxins) described from other pseudoscorpions. Our study yields the first transcriptome of a Beringian arthropod, providing important sequence information that will allow future investigation of how W. asiaticus survives in Canadian polar environments.

scholarly journals Differential requirements of tubulin genes in mammalian forebrain development

2018 ◽  
Author(s):  
Elizabeth Bittermann ◽  
Ryan P. Liegel ◽  
Chelsea Menke ◽  
Andrew Timms ◽  
David R. Beier ◽  
...  
Keyword(s):  
Neural Development ◽  
Human Genetics ◽  
De Novo ◽  
Sequence Similarity ◽  
Large Family ◽  
Missense Variant ◽  
Loss Of Function ◽  
Homologous Proteins ◽  
High Sequence Similarity ◽  
Tubulin Genes

ABSTRACTTubulin genes encode a series of homologous proteins used to construct microtubules which are essential for multiple cellular processes. Neural development is particularly reliant on functional microtubule structures. Tubulin genes comprise a large family of genes with very high sequence similarity between multiple family members. Human genetics has demonstrated that a large spectrum of cortical malformations results from de novo heterozygous mutations in tubulin genes. However, the absolute requirement for most of these genes in development and disease has not been previously tested in genetic, loss of function models. Here we present two novel pathogenic tubulin alleles: a human TUBA1A missense variant with a phenotype more severe than most tubulinopathies and a mouse ENU allele of Tuba1a. Furthermore, we directly test the requirement for Tuba1a, Tuba8, Tubb2a and Tubb2b in the mouse by deleting each gene individually using CRISPR-Cas9 genome editing. We show that loss of Tuba8, Tubb2a or Tubb2b does not lead to cortical malformation phenotypes or impair survival. In contrast, loss of Tuba1a is perinatal lethal and leads to significant forebrain dysmorphology. Thus, despite their functional similarity, the requirements for each of the tubulin genes and levels of functional redundancy are quite different throughout the gene family. The ability of the mouse to survive in the absence of some tubulin genes known to cause disease in humans suggests future intervention strategies for these devastating tubulinopathy diseases.

scholarly journals De-novo chromosome level assembly of plant genomes from long read sequence data

2021 ◽  
Author(s):  
Priyanka Sharma ◽  
Ardashir Kharabian Masouleh ◽  
Bruce Topp ◽  
Agnelo Furtado ◽  
Robert J. Henry
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Genetic Maps ◽  
Sequence Contigs ◽  
Plant Genomes ◽  
Proximity Analysis ◽  
Long Reads ◽  
A Genome ◽  
Long Read ◽  
Chromosome Level

SummaryRecent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. The chromosome level assembly of the contigs generated from long read sequencing has involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (PacBio HiFi) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii. a genome that has been used as model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig and the other 6 assembled into 2-4 main contigs. The small number of chromosome breaks appear to be due to highly repetitive regions of ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now seems possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.Significance statement (of up to two sentences)De novo assembly of near complete chromosome level plant genomes is now possible using current long read sequencing and assembly tools.

scholarly journals Whole genome sequencing of group AStreptococcus: development and evaluation of an automated pipeline foremmgene typing

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3226 ◽  
Author(s):  
Georgia Kapatai ◽  
Juliana Coelho ◽  
Steven Platt ◽  
Victoria J. Chalker
Keyword(s):  
Gold Standard ◽  
De Novo ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Bacterial Strains ◽  
High Sequence Similarity ◽  
England And Wales ◽  
Standard Methodology ◽  
Group A

Streptococcus pyogenesgroup AStreptococcus(GAS) is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS) in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains ofS. pyogenescausing invasive infections and those isolated from patients and healthcare/care workers in cluster and outbreak situations. Sequence analysis of theemmgene is the currently accepted gold standard methodology for GAS typing. A comprehensive database ofemmtypes observed from superficial and invasive GAS strains from England and Wales informs outbreak control teams during investigations. Each year the Bacterial Reference Department, Public Health England (PHE) receives approximately 3,000 GAS isolates from England and Wales. In April 2014 the Bacterial Reference Department, PHE began genomic sequencing of referredS. pyogenesisolates and those pertaining to selected elderly/nursing care or maternity clusters from 2010 to inform future reference services and outbreak analysis (n = 3, 047). In line with the modernizing strategy of PHE, we developed a novel bioinformatics pipeline that can predictemmtypes using whole genome sequence (WGS) data. The efficiency of this method was measured by comparing theemmtype assigned by this method against the result from the current gold standard methodology; concordance toemmsubtype level was observed in 93.8% (2,852/3,040) of our cases, whereas in 2.4% (n = 72) of our cases concordance was observed toemmtype level. The remaining 3.8% (n = 117) of our cases corresponded to novel types/subtypes, contamination, laboratory sample transcription errors or problems arising from high sequence similarity of the allele sequence or low mapping coverage. De novo assembly analysis was performed in the two latter groups (n = 72 + 117) and was able to diagnose the problem and where possible resolve the discordance (60/72 and 20/117, respectively). Overall, we have demonstrated that our WGS emm-typing pipeline is a reliable and robust system that can be implemented to determine emm type for the routine service.

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