Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases

Chung, Charles Wai; Günther, Svenja; Cooke, Brian M.; Coppel, Ross L.

doi:10.1016/j.parint.2012.11.003

Cited by 5 publications

(6 citation statements)

References 12 publications

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“…For gene model estimation, we applied AUGUSTUS version 3.1.0 [ 21 ]. To establish trained parameters for AUGUSTUS, webAugustus [ 27 ] was utilized, and the required data, the genome sequence (PiroplasmaDB-5.1_BbovisT2Bo_Genome.fasta), and the full-length EST (B.bov.FL-EST.fa) for B. bovis were obtained from PiroplasmaDB and DB-AT, respectively [ 28 , 29 ]. The sequences derived from the RNAseq analysis were mapped onto the assembled draft genome sequence of B. ovata with Tophat2.…”

Section: Methodsmentioning

confidence: 99%

Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens

et al. 2017

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Background Babesia ovata, belonging to the phylum Apicomplexa, is an infectious parasite of bovids. It is not associated with the manifestation of severe symptoms, in contrast to other types of bovine babesiosis caused by B. bovis and B. bigemina; however, upon co-infection with Theileria orientalis, it occasionally induces exacerbated symptoms. Asymptomatic chronic infection in bovines is usually observed only for B. ovata. Comparative genomic analysis could potentially reveal factors involved in these distinguishing characteristics; however, the genomic and molecular basis of these phenotypes remains elusive, especially in B. ovata. From a technical perspective, the current development of a very long read sequencer, MinION, will facilitate the obtainment of highly integrated genome sequences. Therefore, we applied next-generation sequencing to acquire a high-quality genome of the parasite, which provides fundamental information for understanding apicomplexans.ResultsThe genome was assembled into 14,453,397 bp in size with 5031 protein-coding sequences (91 contigs and N50 = 2,090,503 bp). Gene family analysis revealed that ves1 alpha and beta, which belong to multigene families in B. bovis, were absent from B. ovata, the same as in B. bigemina. Instead, ves1a and ves1b, which were originally specified in B. bigemina, were present. The B. ovata and B. bigemina ves1a configure one cluster together even though they divided into two sub-clusters according to the spp. In contrast, the ves1b cluster was more dispersed and the overlap among B. ovata and B. bigemina was limited. The observed redundancy and rapid evolution in sequence might reflect the adaptive history of these parasites. Moreover, same candidate genes which potentially involved in the distinct phenotypes were specified by functional analysis. An anamorsin homolog is one of them. The human anamorsin is involved in hematopoiesis and the homolog was present in B. ovata but absent in B. bigemina which causes severe anemia.ConclusionsTaking these findings together, the differences demonstrated by comparative genomics potentially explain the evolutionary history of these parasites and the differences in their phenotypes. Besides, the draft genome provides fundamental information for further characterization and understanding of these parasites.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4230-4) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens

et al. 2017

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“…For comparison, WGS data of Plasmodium spp. (P. falciparum 3D7, P. berghei ANKA [31], P. vivax P01), Piroplasmida (Babesia bovis T2Bo [32], Theileria annulata Ankara [33], Theileria parva Muguga [34]), Coccidia (Eimeria tenella Houghton, Neospora caninum LIV, and Toxoplasma gondii GT1) were obtained from PlasmoDB (https://plasmodb.org/plasmo/) [35], PiroplasmaDB (https://piroplasmadb.org/) [36] and ToxoDB (https://toxodb.org/toxo/) [37] databases, respectively. All genomic data used in this study were the latest updated version.…”

Section: Reference Genomesmentioning

confidence: 99%

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

Roellig

et al. 2023

Microbial Genomics

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Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3–32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.

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“…are publicly available: B. bigemina , B. bovis , B. caballi , B. divergens B. microti , B. ovata , and Babesia sp. Xinjiang ( Brayton et al., 2007 ; Cornillot et al., 2012 ; Ma et al., 2013 ; Jackson et al., 2014 ; Guan et al., 2016 ; Yamagishi et al., 2017 ). In terms of disease control, they contribute to the development of diagnostic methods and vaccines, screening of drug targets, and identification of drug-resistant genes.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequence and diversity in multigene families of Babesia ovis

Yamagishi,

Ceylan,

Xuan

et al. 2023

Front. Cell. Infect. Microbiol.

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Ovine babesiosis, caused by Babesia ovis, is an acute, lethal, and endemic disease worldwide and causes a huge economic loss to animal industry. Pathogen genome sequences can be utilized for selecting diagnostic markers, drug targets, and antigens for vaccine development; however, those for B. ovis have not been available so far. In this study, we obtained a draft genome sequence for B. ovis isolated from an infected sheep in Turkey. The genome size was 7.81 Mbp with 3,419 protein-coding genes. It consisted of 41 contigs, and the N50 was 526 Kbp. There were 259 orthologs identified among eight Babesia spp., Plasmodium falciparum, and Toxoplasma gondii. A phylogeny was estimated on the basis of the orthologs, which showed B. ovis to be closest to B. bovis. There were 43 ves genes identified using hmm model as well. They formed a discriminating cluster to other ves multigene family of Babesia spp. but showed certain similarities to those of B. bovis, B. caballi, and Babesia sp. Xinjiang, which is consistent with the phylogeny. Comparative genomics among B. ovis and B. bovis elucidated uniquely evolved genes in these species, which may account for the adaptation.

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Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases

Cited by 5 publications

References 12 publications

Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens

Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens

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

Whole genome sequence and diversity in multigene families of Babesia ovis

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