scholarly journals The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens

2018 ◽  
Author(s):  
Sebastián Pita ◽  
Florencia Díaz-Viraqué ◽  
Gregorio Iraola ◽  
Carlos Robello
Keyword(s):  
Repetitive Dna ◽  
Leishmania Major ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Low Cost ◽  
Repetitive Sequences ◽  
Human Pathogens ◽  
Genome Wide ◽  
Low Coverage

AbstractThe major human pathogens Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously unknown transposable element in Leishmania major (TATE family), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozooan genomes.

scholarly journals Development and Characterization of SSR Markers in the Gossypium Barbadense Genome

2021 ◽  
Author(s):  
Wenjuan ZHONG ◽  
Can YUAN ◽  
Zhengjie CHEN ◽  
Yonghang ZHOU ◽  
Siwei Chen ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Low Cost ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Pcr Analysis ◽  
Genetic Studies ◽  
Genome Wide ◽  
User Friendly

Abstract BackgroundThe fiber quality and resistance traits of Gossypium barbadense are considerably better than that of other Gossypium species. Simple sequence repeats (SSRs) are user friendly, low cost markers widely used in genetic studies. However, most SSRs have been developed from G. hirsutum, G. arboreum, and G. raimondii; no genome-wide SSRs have been developed from G. barbadense.The de novo sequences of G. barbadense cv. Xinhai21 were utilized to develop SSR markers and scanned to detect SSRs using the MIcroSAtellite (http://pgrc.ipk-gatersleben.de/misa/) identification tool. And then in silico PCR analysis was conducted to evaluate these primers polymorphism in five Gossypium species.ResultsIn total, 85,582 SSRs were identified with different motifs. 153,560 primer pairs were successfully designed for 73,419 SSRs. In silico analysis, we found that 8,466 primer pairs of 3,288 SSRs yielded one product (monomorphic) simultaneously in five Gossypium species. two Gossypium species (30 G. hirsutum and 27 G. barbadense accessions) were successfully separated by 300 primer pairs with the polymorphism information content (PIC) ranging from 0.00 to 0.93. ConclusionThese newly developed SSR markers will be helpful for the construction of genetic linkage maps, genetic diversity analyses, QTL mapping, and molecular breeding of Gossypium species.

scholarly journals Purine Nucleobase Transport in Amastigotes of Leishmania mexicana: Involvement in Allopurinol Uptake

2005 ◽  
Vol 49 (9) ◽  
pp. 3682-3689 ◽  
Author(s):  
Mohammed I. Al-Salabi ◽  
Harry P. de Koning
Keyword(s):  
Leishmania Major ◽  
De Novo ◽  
Nucleoside Transporters ◽  
Human Pathogens ◽  
Leishmania Mexicana ◽  
Purine Analogues ◽  
Purine Salvage ◽  
High Affinity ◽  
Identification And Characterization

ABSTRACT Nucleobase and nucleoside transporters play central roles in the biochemistry of parasitic protozoa, as they lack the ability to synthesize purines de novo and are absolutely reliant upon purine salvage from their hosts. Furthermore, such transporters are potentially critical to the pharmacology of these important human pathogens, because they mediate the uptake of purine analogues, as well as some nonpurine drugs, that can be selectively cytotoxic to the parasites. We here report the first identification and characterization of a purine nucleobase transporter in Leishmania amastigotes. Uptake of [3H]hypoxanthine by Leishmania mexicana amastigotes was mediated by a single high-affinity transporter, LmexNBT1, with a Km of 1.6 ± 0.4 μM and high affinity for adenine, guanine, and xanthine but low affinity for nucleosides and pyrimidine nucleobases. Allopurinol, an antileishmanial hypoxanthine analogue, was apparently taken up by the same transporter. Using [3H]allopurinol, a Km value of 33.6 ± 6.0 μM was obtained. All evidence was compatible with a model of a single purine nucleobase transporter being expressed in amastigotes. Using various purine nucleobase analogues, a model for the interactions between hypoxanthine and the transporter's permeant binding site was constructed. The binding interactions were compared with those of the LmajNBT1 transporter in Leishmania major promastigotes and found to be very similar.

scholarly journals Correction to: low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vanessa Carvalho Cayres Pamponét ◽  
Margarete Magalhães Souza ◽  
Gonçalo Santos Silva ◽  
Fabienne Micheli ◽  
Cláusio Antônio Ferreira de Melo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Satellite Dna ◽  
Dna Analysis ◽  
Passiflora Edulis ◽  
Passiflora Edulis Sims ◽  
Low Coverage

scholarly journals Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage

2021 ◽  
Author(s):  
Tilman Rönneburg ◽  
Yanjun Zan ◽  
Christa F Honaker ◽  
Paul B Siegel ◽  
Örjan Carlborg
Keyword(s):  
Body Weight ◽  
Complex Traits ◽  
Low Cost ◽  
Minor Effect ◽  
Genome Coverage ◽  
Selection Responses ◽  
Genome Wide ◽  
Low Coverage ◽  
Experimental Crosses

Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation, often the F2, with additional, later generation individuals being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, divergent bi-directional selection responses for 56-day body weight in the Virginia chicken lines. To achieve this, a powerful strategy was developed to make use of data from all generations (F2-F18) of an advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for >3,300 intercross individuals. In total, 12 genome-wide significant and 10 additional suggestive QTL for 56-day body weight were mapped, with only two of these QTL reaching genome-wide, and one suggestive, significance in analyses of the F2 generation. Five of the significant, and four of the suggestive, QTL were among the 20 loci reaching a 20% FDR-threshold in previous analyses of data from generation F15. The novel, minor-effect QTL mapped here were generally mapped due to an overall increase in power by integrating data across generations, with minor contributions from increased genome-coverage and improved marker information content. Significant and suggestive QTL now explain >60% of the difference between the parental lines, three times more than the previously reported significant QTL. Making integrated use of all available samples from multiple generations in experimental crosses is now economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-day body weight in the Virginia chicken lines.

scholarly journals Full Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak Investigation

2020 ◽  
Vol 58 (12) ◽  
Author(s):  
Mark Itsko ◽  
Adam C. Retchless ◽  
Sandeep J. Joseph ◽  
Abigail Norris Turner ◽  
Jose A. Bazan ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Molecular Typing ◽  
De Novo ◽  
Multiple Displacement Amplification ◽  
Low Cost ◽  
Vaccine Antigen ◽  
Content Type ◽  
Clinical Specimens ◽  
Low Culture

ABSTRACT Neisseria meningitidis is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens, such as cerebrospinal fluid (CSF), blood, or urine. However, genome sequencing of specimens is challenging because of low bacterial and high human DNA abundances. We developed selective whole-genome amplification (SWGA), an isothermal multiple-displacement amplification-based method, to efficiently enrich, sequence, and de novo assemble N. meningitidis DNA from clinical specimens with low bacterial loads. SWGA was validated with 12 CSF specimens from invasive meningococcal disease cases and 12 urine specimens from meningococcal urethritis cases. SWGA increased the mean proportion of N. meningitidis reads by 2 to 3 orders of magnitude, enabling identification of at least 90% of the 1,605 N. meningitidis core genome loci for 50% of the specimens. The validated method was used to investigate two meningitis outbreaks recently reported in Togo and Burkina Faso. Twenty-seven specimens with low bacterial loads were processed by SWGA before sequencing, and 12 of 27 were successfully assembled to obtain the full molecular typing and vaccine antigen profile of the N. meningitidis pathogen, thus enabling thorough characterization of outbreaks. This method is particularly important for enhancing molecular surveillance in regions with low culture rates. SWGA produces enough reads for phylogenetic and allelic analysis at a low cost. More importantly, the procedure can be extended to enrich other important human bacterial pathogens.

scholarly journals Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis

2020 ◽  
Vol 37 (5) ◽  
pp. 1362-1375 ◽  
Author(s):  
Jullien M Flynn ◽  
Manyuan Long ◽  
Rod A Wing ◽  
Andrew G Clark
Keyword(s):  
Evolutionary Dynamics ◽  
Repetitive Sequences ◽  
Pericentromeric Region ◽  
Drosophila Virilis ◽  
Sequencing Data ◽  
Satellite Sequence ◽  
Sequence Composition ◽  
Rapid Changes ◽  
Multiple Strains

Abstract The factors that drive the rapid changes in abundance of tandem arrays of highly repetitive sequences, known as satellite DNA, are not well understood. Drosophila virilis has one of the highest relative amounts of simple satellites of any organism that has been studied, with an estimated >40% of its genome composed of a few related 7-bp satellites. Here, we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the highly abundant AAACTAC satellite family arose from a related satellite in the branch leading to the virilis phylad 4.5–11 Ma before exploding in abundance in some species of the clade. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. By analyzing multiple strains of D. virilis, we saw that the abundances of two centromere-proximal satellites are anticorrelated along a geographical gradient, which we suggest could be caused by ongoing conflicts at the centromere. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes including selection, meiotic drive, and constraints on satellite sequence and abundance.

scholarly journals Assembly of the Mitochondrial Genome in the Campanulaceae Family Using Illumina Low-Coverage Sequencing

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 383 ◽  
Author(s):  
Hyun-Oh Lee ◽  
Ji-Weon Choi ◽  
Jeong-Ho Baek ◽  
Jae-Hyeon Oh ◽  
Sang-Choon Lee ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Dna Sequencing ◽  
De Novo ◽  
Genome Structure ◽  
Sequencing Data ◽  
Phylogenetic Characterization ◽  
Low Coverage ◽  
Paired End Sequencing ◽  
Circular Chromosomes

Platycodon grandiflorus (balloon flower) and Codonopsis lanceolata (bonnet bellflower) are important herbs used in Asian traditional medicine, and both belong to the botanical family Campanulaceae. In this study, we designed and implemented a de novo DNA sequencing and assembly strategy to map the complete mitochondrial genomes of the first two members of the Campanulaceae using low-coverage Illumina DNA sequencing data. We produced a total of 28.9 Gb of paired-end sequencing data from the genomic DNA of P. grandiflorus (20.9 Gb) and C. lanceolata (8.0 Gb). The assembled mitochondrial genome of P. grandiflorus was found to consist of two circular chromosomes; the master circle contains 56 genes, and the minor circle contains 42 genes. The C. lanceolata mitochondrial genome consists of a single circle harboring 54 genes. Using a comparative genome structure and a pattern of repeated sequences, we show that the P. grandiflorus minor circle resulted from a recombination event involving the direct repeats of the master circle. Our dataset will be useful for comparative genomics and for evolutionary studies, and will facilitate further biological and phylogenetic characterization of species in the Campanulaceae.

scholarly journals Topologically Dependent Abundance of Spontaneous DNA Damage in Single Human Cells

2019 ◽  
Author(s):  
Qiangyuan Zhu ◽  
Yichi Niu ◽  
Michael Gundry ◽  
Kuanwei Sheng ◽  
Muchun Niu ◽  
...  
Keyword(s):  
Dna Damage ◽  
Single Cell ◽  
Genome Stability ◽  
De Novo ◽  
Single Cells ◽  
Human Cells ◽  
Single Nucleotide Variants ◽  
Genome Wide ◽  
First Time

AbstractIn the studies of single-cell genomics, the large endeavor has been focused on the detection of the permanent changes in the genome. On the other hand, spontaneous DNA damage frequently occurs and results in transient single-stranded changes to the genome until they are repaired. So far, successful profiling of these dynamic changes has not been demonstrated by single-cell whole-genome amplification methods. Here we reported a novel single-cell WGA method: Linearly Produced Semiamplicon based Split Amplification Reaction (LPSSAR), which allows, for the first time, the genome-wide detection of the DNA damage associated single nucleotide variants (dSNVs) in single human cells. The sequence-based detection of dSNVs allows the direct characterization of the major damage signature that occurred in human cells. In the analysis of the abundance of dSNVs along the genome, we observed two modules of dSNV abundance, instead of a homogeneous abundance of dSNVs. Interestingly, we found that the two modules are associated with the A/B topological compartments of the genome. This result suggests that the genome topology directly influences genome stability. Furthermore, with the detection of a large number of dSNVs in single cells, we showed that only under a stringent filtering condition, can we distinguish the de novo mutations from the dSNVs and achieve a reliable estimation of the total level of de novo mutations in a single cell.

scholarly journals Evolutionary Characterization of the Short Protein SPAAR

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1864
Author(s):  
Jiwon Lee ◽  
Aaron Wacholder ◽  
Anne-Ruxandra Carvunis
Keyword(s):  
Muscle Regeneration ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Sequence Divergence ◽  
Biological Processes ◽  
Noncoding Sequence ◽  
Homology Detection ◽  
Evolutionary Innovation ◽  
Short Protein

Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs exclusively among placental mammals. This lack of distant homology could be caused by challenges in homology detection of short sequences, or it could indicate a recent de novo emergence from a noncoding sequence. By integrating syntenic alignments and homology searches, we identify SPAAR orthologs in marsupials and monotremes, establishing that SPAAR has existed at least since the emergence of mammals. SPAAR shows substantial primary sequence divergence but retains a conserved protein structure. In primates, we infer two independent evolutionary events leading to the de novo origination of 5′ elongated isoforms of SPAAR from a noncoding sequence and find evidence of adaptive evolution in this extended region. Thus, SPAAR may be of ancient origin, but it appears to be experiencing continual evolutionary innovation in mammals.

scholarly journals Mining SNPs From EST Databases

1999 ◽  
Vol 9 (2) ◽  
pp. 167-174 ◽  
Author(s):  
Leslie Picoult-Newberg ◽  
Trey E. Ideker ◽  
Mark G. Pohl ◽  
Scott L. Taylor ◽  
Miriam A. Donaldson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
De Novo ◽  
Cdna Libraries ◽  
Human Populations ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Using Data

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.[The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).]

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