scholarly journals An Improved Genome Assembly for Drosophila navojoa, the Basal Species in the mojavensis Cluster

2018 ◽  
Vol 110 (1) ◽  
pp. 118-123 ◽  
Author(s):  
Thyago Vanderlinde ◽  
Eduardo Guimarães Dupim ◽  
Nestor O Nazario-Yepiz ◽  
Antonio Bernardo Carvalho
Keyword(s):  
Genome Assembly ◽  
Chromosomal Rearrangements ◽  
Substantial Improvement ◽  
Insert Size ◽  
Genetic Studies ◽  
Cactophilic Drosophila ◽  
Host Shifts ◽  
Evolutionary Genetic ◽  
Relationship Of ◽  
Assembly Software

Abstract Three North American cactophilic Drosophila species, D. mojavensis, D. arizonae, and D. navojoa, are of considerable evolutionary interest owing to the shift from breeding in Opuntia cacti to columnar species. The 3 species form the “mojavensis cluster” of Drosophila. The genome of D. mojavensis was sequenced in 2007 and the genomes of D. navojoa and D. arizonae were sequenced together in 2016 using the same technology (Illumina) and assembly software (AllPaths-LG). Yet, unfortunately, the D. navojoa genome was considerably more fragmented and incomplete than its sister species, rendering it less useful for evolutionary genetic studies. The D. navojoa read dataset does not fully meet the strict insert size required by the assembler used (AllPaths-LG) and this incompatibility might explain its assembly problems. Accordingly, when we re-assembled the genome of D. navojoa with the SPAdes assembler, which does not have the strict AllPaths-LG requirements, we obtained a substantial improvement in all quality indicators such as N50 (from 84 kb to 389 kb) and BUSCO coverage (from 77% to 97%). Here we share a new, improved reference assembly for D. navojoa genome, along with a RNAseq transcriptome. Given the basal relationship of the Opuntia breeding D. navojoa to the columnar breeding D. arizonae and D. mojavensis, the improved assembly and annotation will allow researchers to address a range of questions associated with the genomics of host shifts, chromosomal rearrangements and speciation in this group.

scholarly journals A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

2021 ◽  
Author(s):  
Seyoung Mun ◽  
Songmi Kim ◽  
Wooseok Lee ◽  
Keunsoo Kang ◽  
Thomas J. Meyer ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Personal Genome ◽  
Human Populations ◽  
Whole Genome ◽  
Structural Variations ◽  
Insert Size ◽  
Human Genomes ◽  
Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

RELATIONSHIP OF TAXA IN THE GENUS MEDICAGO AS REVEALED BY HYBRIDIZATION. I. M. STRIATA × M. LITTORALIS

1968 ◽  
Vol 10 (2) ◽  
pp. 263-275 ◽  
Author(s):  
K. Lesins ◽  
A. Erac
Keyword(s):  
High Mortality ◽  
Genetic Factor ◽  
Genetic Factors ◽  
Chromosomal Rearrangements ◽  
Cytoplasmic Factor ◽  
Reciprocal Crosses ◽  
Gross Chromosomal Rearrangements ◽  
Coiling Direction ◽  
Chlorophyll Deficiencies ◽  
Relationship Of

In crosses between the two taxa Medicago striata Bast, and M. littoralis Rohde a high mortality of gametes and seedlings, and sterility of some plants were noted which were not related to gross chromosomal rearrangements. Although the F1, F2 and F3 generations from reciprocal crosses differed in chlorophyll deficiencies (indicating a cytoplasmic influence) a genic cause became evident from segregations for chlorophyll characters in the F2 and F3. Transference of the cytoplasmic factor by the pollen is indicative.Segregation for pod coiling direction indicated that the character was determined by one or two genetic factors of which the clockwise coiling direction is recessive. The spininess appeared to be determined by one genetic factor, of which the spineless allele is recessive.On the basis of genetic differences (especially on the built-in repulsion systems for normal chlorophyll development of opposite species) the two taxa should be considered two different species.

scholarly journals Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

2021 ◽  
Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Southwest China ◽  
Reference Genome ◽  
Biological Activities ◽  
Single Copy ◽  
The Tibetan Plateau ◽  
Whole Genome ◽  
High Quality ◽  
Pharmacological Activities ◽  
Genetic Studies

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

scholarly journals Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12446
Author(s):  
Darlene D. Wagner ◽  
Heather A. Carleton ◽  
Eija Trees ◽  
Lee S. Katz
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Enteric Bacteria ◽  
Quality Metrics ◽  
Read Length ◽  
Snp Analysis ◽  
Whole Genome ◽  
Insert Size ◽  
E Coli

Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality. Methods Raw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters. Results Assembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads. Conclusions PHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies.

scholarly journals Cytogenetics of two Farlowella species (Loricariidae: Loricariinae): implications on the taxonomic status of the species

2018 ◽  
Vol 16 (4) ◽  
Author(s):  
Leandro Marajó ◽  
Patrik F. Viana ◽  
Milena Ferreira ◽  
Lúcia H. Rapp Py-Daniel ◽  
Eliana Feldberg
Keyword(s):  
Chromosome Number ◽  
Species Complex ◽  
Chromosomal Rearrangements ◽  
5S Rdna ◽  
Taxonomic Status ◽  
Specific Marker ◽  
Genetic Studies ◽  
Molecular Cytogenetic ◽  
Metacentric Pair ◽  
Species Specific

ABSTRACT Farlowella is one of the most diverse genera of the Loricariinae, restricted to South America rivers. The taxonomic and phylogenetic relationships among its species are contentious and, while genetic studies would contribute to the understanding of their relationships, the only available datum refer to the karyotype description of only one species. In the present study two Amazonian species, Farlowella cf. amazonum and F. schreitmuelleri, were analyzed using conventional and molecular cytogenetic procedures. Both species had diploid chromosome number 58, but different fundamental numbers (NF) 116 and 112, respectively, indicative of chromosomal rearrangements. C-banding is almost poor, especially in F. cf. amazonum, and occurs predominantly in the centromeric and in some telomeric regions, although genome of F. schreitmuelleri possessed a much larger heterochromatin amount then those of F. cf. amazonum. The chromosomes bearing the NOR sites were likely the same for both species, corresponding to the 1st metacentric pair in F. cf. amazonum and to the 28th acrocentric in F. schreitmuelleri. The location of the 5S rDNA was species-specific marker. This study expanded the available cytogenetic data for Farlowella species and pointed the remarkable karyotype diversity among species/populations, indicating a possible species complex within genus.

Molecular, developmental, and evolutionary genetic studies highlight rapid evolution of genes and genetic systems

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 848-852
Author(s):  
Jianping Xu
Keyword(s):  
Large Scale ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Annual Conference ◽  
Genetic Studies ◽  
The Us ◽  
Evolutionary Genetic ◽  
Genetic Systems ◽  
Oral Presentations ◽  
The Impact

The 53rd annual conference of the Genetics Society of Canada was held at McMaster University in Hamilton, Ontario, from 17 to 20 June 2010. About 100 geneticists from across Canada and the US attended the meeting, with a total of 27 posters and 55 oral presentations. The presentations highlighted the power of genetics for understanding a variety of biological issues from sex and recombination to alcoholism and cancer, from DNA replication to antimicrobial resistance, horizontal gene transfer, foraging, and courtship. Large-scale genomic and transcriptomic comparisons were included in many presentations to demonstrate the impact of genomics in biomedical research. The combined molecular, developmental, and evolutionary genetic investigations presented at the meeting, especially those on model organisms, highlighted that genes and genetic systems can evolve very rapidly.

scholarly journals SWALO: scaffolding with assembly likelihood optimization

2016 ◽  
Author(s):  
Atif Rahman ◽  
Lior Pachter
Keyword(s):  
Maximum Likelihood ◽  
Genome Assembly ◽  
Statistical Models ◽  
Substantial Improvement ◽  
Generative Models ◽  
Large Datasets ◽  
Maximum Likelihood Estimates ◽  
Link Type ◽  
Genome Assemblies

AbstractScaffolding i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding based on likelihoods of genome assemblies. Generative models for sequencing are used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.

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