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Genome assembly

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Enhanced genome assembly and a new official gene set for Tribolium castaneum

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However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality.. Results: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources.

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

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For example, two regions of different chromosomes (RACA_21 and RACA_24) in the previous assembly mapped to contig439 of the current genome assembly (Fig. Two chromosomes (RACA_21, RACA_24) of the previous assembly mapped to this contig. Two chromosomes (RACA81, RACA_11) of the previous assembly mapped to this contig. As a species of the genus Oryzias, O.. melastigma and the protein sets of the above 17 species.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

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Chromosome-length genome assembly and structural variations of the primal Basenji dog ( Canis lupus familiaris ) genome. CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. Full list of author information is available at the end of the article.

Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica

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Assembly of the HM-1:IMSS clone 6 2001 reference genome. The workflow for genome assembly is shown in a flow diagram [Extended Data 1 (Additional file 1. After scaffolding, we filled in gaps in the assembly using PBjelly. The genome was temporally annotated by Companion.. Additional file 1: Extended Data 1-4.. TKS and SI analyzed and interpreted the genome data.

A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi

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Analysis of the repeat con- tent of the chromosome-scale assembly of P. Most of the repeat elements identified were found in simple re- peat sequences (0.278%) (Table S3). Only 0.05% of the genome assembly was classified as transposable element (TE) insertions. Most of the TE insertions were from retroelements (86.6. 5a), so no full-length TE was detected in the P.

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linkedreads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

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The assembly presented here will enormously boost the understanding of the olive fruit fly’s biology and genome. The highly repetitive nature of the Y chromosome makes it the most challenging to assemble in genome sequencing efforts. Gene expression (transcripts per million) was calculated for each of the 4 metamorphotic stages. Breeding of the insects. To generate an ONT based assembly, ONT sequence reads were used for de novo genome assembly of the olive fly using Canu [121]..

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

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Genome sequencing, assembly, and annotation of the self-flocculating. microalga Scenedesmus obliquus AS-6-11. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Comparing to the genome sequences of the well-studied green microalgae. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin.

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

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Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster. Results: Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10. hongkongensis genome of Peng et al.. Full list of author information is available at the end of the article.

Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

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Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. De novo assembly of the cattle reference genome with single-molecule sequencing. Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle. A whole-genome assembly of the domestic cow, Bos taurus

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

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Results: To fill this gap, we generated a chromosome-level genome assembly of the S.

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations

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Sequencing and assembly of the 22-gb loblolly pine genome. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Assessing genome assembly quality using the LTR Assembly Index (LAI). Versatile genome assembly evaluation with QUAST-LG. https://doi.org/10.1093/bioinformatics/bty266..

Genome sequence of the model rice variety KitaakeX

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To obtain a high-quality, de novo genome assembly, we sequenced the KitaakeX genome using a strategy that combines short-read and long-read sequencing. We assessed the quality of the KitaakeX assembly for sequence completeness and accuracy. Complete- ness of the assembly was assessed by aligning the 34, 651 annotated genes from the v7.0 Nipponbare to the KitaakeX assembly using BLAT [24].

Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline

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The current state-of-the-art genome assembly approach, termed hybrid assembly, leverages benefits of both long, relatively error-prone reads from third-generation sequencing technologies, and short, ac- curate reads from second-generation sequencing tech- nologies to produce more accurate and contiguous de novo genome assemblies than could be achieved using either technology independently [8]. brunneum isolate ARSEF 4556, as well as the generation of the full circular mitochondrial genome.

The effect of variant interference on de novo assembly for viral deep sequencing

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Reference-mapping and de novo as- sembly are the two primary bioinformatic strategies for genome assembly. Reference-mapping requires a closely- related genome as input to align reads, while de novo as- sembly generates contigs without the use of a reference genome. Therefore, de novo assembly is the most suitable strategy for analyzing underexplored taxa [16] or for vi- ruses with high mutation and/or recombination rates..

Comparative genome characterization of the periodontal pathogen Tannerella forsythia

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Improved assembly of the Tannerella forsythia type strain ATCC 43037. The genome of the T. The largest sequence was 487 kbp comprising about 15% of the total assembly size of 3.282 Megabase- pairs (Mbp). We used both the published paired-end se- quencing reads downsampled to a coverage of 100-fold and the newly generated mate-pairs to build connections between the contigs of the ATCC 43037 genome assembly generated by Friedrich et al.

The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity

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Table 1 Summary of the Tachypleus tridentatus genome assembly and annotation statistic. Summary of the Tachypleus tridentatus genome assembly and annotation statistics.. a of 1066 arthropod BUSCOs Complete [Duplicated], Fragmented, Missing, in the assembly. To determine the reliabil- ity of the repeat contents screening by RepeatMasker and RepeatModeler, we also performed repeat analysis of the L.

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

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Further analysis was carried out using the first 161,667 bp of the genome assembly.. Comparison of methods for annotation of cp genome for cv Tombul. The cv Tombul cp genome presented similar character- istics to other angiosperm cp genomes. While the general characteristics of cv Tom- bul cp genome are highly consistent with KX822768, a few differences were detected at the gene level. sequences were predicted for these genes in the cv Tom- bul cp genome.

The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: Insights into the chloroplast evolution and transcription regulation

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Chloroplast genome assembly, validation and annotation The last version of the complete chloroplast genome of S.polyrhiza 7498 (SpV1) was sequenced on a SOLiD platform and published in 2011 (GenBank accession number: JN .

Genome of extreme halophyte Puccinellia tenuiflora

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Moreover, completeness of the assembly also was assessed using BUSCO [63] combined with TBLASTN [46], Augustus (version and HMMER (version 3.1b2) [64]. The genome assembly of P. tenuiflora consisted of 14, 036 contigs with a total size of 1.095 Gb. Finally, we as- sembled 2638 scaffolds with a total size of 1.107 Gb, contig N50 of 117 kb, and scaffold N50 of 950 kb.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

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Genome comparison of Siberian musk deer and forest musk deer. We compared the genome assembly of the Siberian musk deer and forest musk deer recently reported by Fan et al.. The continuity of our assembly was remarkably increased compared with that of the forest musk deer genome assembly, particularly in re- gard to the scaffold N50 (7.95 vs 2.85 Mb) and scaffold number (13,344 vs 79,206).