Comparison of Functional Gene Annotation of Toxascaris leonina and Toxocara canis using CLC Genomics Workbench

Abstract

The ascarids, Toxocara canis and Toxascaris leonina, are probably the most common gastrointestinal helminths encountered in dogs. In order to understand biological differences of 2 ascarids, we analyzed gene expression profiles of female adults of T. canis and T. leonina using CLC Genomics Workbench, and the results were compared with those of free-living nematode Caenorhabditis elegans. A total of 2,880 and 7,949 ESTs were collected from T. leonina and T. canis, respectively. The length of ESTs ranged from 106 to 4,637 bp with an average insert size of 820 bp. Overall, our results showed that most functional gene annotations of 2 ascarids were quite similar to each other in 3 major categories, i.e., cellular component, biological process, and molecular function. Although some different transcript expression categories were found, the distance was short and it was not enough to explain their different lifestyles. However, we found distinguished transcript differences between ascarid parasites and free-living nematodes. Understanding evolutionary genetic changes might be helpful for studies of the lifestyle and evolution of parasites.

High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species

“…FastQC (https://qubeshub.org/resources/fastqc) [41] was used to remove the low-quality bases (score <20) from the sequencing reads, and adapter sequences were trimmed by using Trimmomatic 0.36 (https://github.com/usadellab/Trimmomatic/releases) [42]. The CLC Genomics Workbench 11 (https://www.qiagenbioinformatics.com/products/clc-genomics-workbench) [14] was used in the de novo assembly of the genomes with the word size of 63 and bubble size of 500. Contigs from contaminants were removed from the assembled genomes by searching against the NCBI nt database (https://ftp.ncbi.nlm.nih.gov/blast/db/v5/v4/) using blastn v2.2.31 (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+) [43].…”

“…Whole-genome sequencing and comparative genomic analysis have been used in delineating the genetic basis for differences in host range among Cryptosporidium species and host adaptation within individual species [12][13][14]. To date, the genomes of more than 14 Cryptosporidium species have been sequenced [12,[15][16][17] and these data are available in CryptoDB (https://cryptodb.…”

The Combination of Phages and Faecal Microbiota Transplantation Can Effectively Treat Mouse Colitis Caused by Salmonella enterica Serovar Typhimurium

“…The presence of tRNA was detected by a transcanner. 1 CLC Genomics Workbench 8.1 (CLC Bio-Qiagen, Aarhus, Denmark) was used to visualise the functional models of the genome ( Kim et al, 2013 ). MEGA version 7.0.26 ( Hall, 2013 ) was used to analyse the evolutionary relationship between isolated phages and reported phages based on the amino acid sequence of the terminal enzyme large subunits ( Casjens et al, 2005 ).…”

Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

“…Raw reads were filtered using the NGS QC Toolkit v. 2.3.3 [ 33 ] with a cut-off value of 80 for the percentage of read lengths and a cut-off value of 30 for PHRED quality scores. The plastome assembly, using the high-quality clean reads, was conducted using CLC genomics workbench 8 [ 34 ] and SOAPdenovo [ 35 ] with a k mer of 63 and a minimum overlap length of 1 kb. The plastome of Physalis peruviana (GenBank accession number: MH019242) was used as the reference sequence for genome assembly.…”