Genome Sequence of
            <i>Trypanosoma cruzi</i>
            Strain Bug2148

Callejas-Hernández, Francisco; Gironès, Núria; Fresno, Manuel

doi:10.1128/genomea.01497-17

Cited by 16 publications

(15 citation statements)

References 12 publications

(11 reference statements)

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“…For example, while TcI genome sequences from the US or Panama formed single clusters, those from Colombia or Venezuela could be found in very distinct clusters. Finally, whole genome analysis further indicated that the genome of “Bug2148” clearly belonged to TcI, and was more closely related to the Dm28c and SylvioX10 strains ( Figure 1 ), while this strain was initially sequenced as TcV [ 43 ]. On the other hand, strain H1 from Panama was associated with the TcVI DTU cluster rather than to TcI as initially classified [ 17 ].…”

Section: Resultsmentioning

confidence: 99%

“…The parasite is predominantly described as diploid, with recently reported haploid genomes of 55 Mb [ 43 ] and 79 Mb [ 44 ] in length from DTUs TcI and TcV, respectively. However, the genome is markedly plastic, with genome size and karyotypic variation between strains, irregular genetic exchange, and reports of widespread aneuploidy [ 45 , 46 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics

et al. 2021

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Chagas disease is an important vector-borne neglected tropical disease that causes great health and economic losses. The etiological agent, Trypanosoma cruzi, is a protozoan parasite endemic to the Americas, comprised by important diversity, which has been suggested to contribute to poor serological diagnostic performance. Current nomenclature describes seven discrete typing units (DTUs), or lineages. We performed the first large scale analysis of T. cruzi diversity among 52 previously published genomes from strains covering multiple countries and parasite DTUs and assessed how different markers summarize this genetic diversity. We also examined how seven antigens currently used in commercial serologic tests are conserved across this diversity of strains. DTU structuration was confirmed at the whole-genome level, with evidence of sub-DTU diversity, associated in part to geographic structuring. We observed very comparable phylogenetic tree topographies for most of the 32 markers investigated, with clear clustering of sequences by DTU, and a few of these markers suggested some degree of intra-lineage diversity. At least three of the currently used antigens represent poorly conserved sequences, with sequences used in tests quite divergent from sequences in many strains. Most markers are well suited for estimating parasite diversity to DTU level, and a few are particularly well-suited to assess intra-DTU diversity. Analysis of antigen sequences across all strains indicates that antigenic diversity is a likely explanation for limited diagnostic performance in Central and North America.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics

et al. 2021

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“…Genome from Bug2148 was sequenced with Pacific Biosciences (PacBio) technologies at the Norwegian Sequencing Centre ( www.sequencing.uio.no ), a national technology platform hosted by the University of Oslo and supported by the “Functional Genomics” and “Infrastructure” programs of the Research Council of Norway and the Southeastern Regional Health Authorities 67 . Y strain was sequenced with Illumina MiSeq series by the Genomics facility at the Parque Científico de Madrid (PCM, Madrid, Spain).…”

Section: Methodsmentioning

confidence: 99%

Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity

Callejas-Hernández

Rastrojo

Poveda

et al. 2018

Sci Rep

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Chagas disease is a complex illness caused by the protozoan Trypanosoma cruzi displaying highly diverse clinical outcomes. In this sense, the genome sequence elucidation and comparison between strains may lead to disease understanding. Here, two new T. cruzi strains, have been sequenced, Y using Illumina and Bug2148 using PacBio, assembled, analyzed and compared with the T. cruzi annotated genomes available to date. The assembly stats from the new sequences show effective improvement of T. cruzi genome over the actual ones. Such as, the largest contig assembled (1.3 Mb in Bug2148) in de novo attempts and the highest mean assembly coverage (71X for Y). Our analysis reveals a new genomic expansion and greater complexity for those multi-copy gene families related to infection process and disease development, such as Trans-sialidases, Mucins and Mucin Associated Surface Proteins, among others. On one side, we demonstrate that multi-copy gene families are located near telomeric regions of the “chromosome-like” 1.3 Mb contig assembled of Bug2148, where they likely suffer high evolutive pressure. On the other hand, we identified several strain-specific single copy genes that might help to understand the differences in infectivity and physiology among strains. In summary, our results indicate that T. cruzi has a complex genomic architecture that may have promoted its evolution.

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“…This could lead to over-, under- or miss-representation of genes or complete chromosomic regions. In this regard, long-read sequencing methods (i.e., PacBio, Nanopore) could be a better choice for the trypanosomatids genomes [ 52 ], as the case of Bug2148 strain [ 53 ]. This technology allows the sequencing of long genetic fragments avoiding the complex and repetitive nature of the parasite.…”

Section: The Genomes Of T Cruzi : a New Updatementioning

confidence: 99%

“…Full length chromosome sequencing was performed with this hybrid strain, using a combined strategy based on bacterial artificial chromosome (BAC) ends sequencing and synteny maps with T. brucei [ 58 ], obtaining 41 virtual chromosomes ( Table 1 ). Despite the continuous re-annotations of these genomes, they are far from being the best reference considering all the new and more completed genomes obtained with current techniques of long and short-read sequencing as Y [ 47 ], Bug2148 [ 53 ], Berenice [ 54 ] or Dm28c [ 55 ] strains. Therefore, we need to pose again which genome is appropriate as a reference for T. cruzi research and if the existence of just one genome reference is useful due to the high heterogeneity of the parasite.…”

Section: The Genomes Of T Cruzi : a New Updatementioning

confidence: 99%

Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

Herreros-Cabello

Callejas-Hernández

Gironès

et al. 2020

Genes

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Chagas disease caused by the parasite Trypanosoma cruzi affects millions of people. Although its first genome dates from 2005, its complexity hindered a complete assembly and annotation. However, the new sequencing methods have improved genome annotation of some strains elucidating the broad genetic diversity and complexity of this parasite. Here, we reviewed the genomic structure and regulation, the genetic diversity, and the analysis of the principal multi-gene families of the recent genomes for several strains. The telomeric and sub-telomeric regions are sites with high recombination events, the genome displays two different compartments, the core and the disruptive, and the genome plasticity seems to play a key role in the survival and the infection process. Trypanosoma cruzi (T. cruzi) genome is composed mainly of multi-gene families as the trans-sialidases, mucins, and mucin-associated surface proteins. Trans-sialidases are the most abundant genes in the genome and show an important role in the effectiveness of the infection and the parasite survival. Mucins and MASPs are also important glycosylated proteins of the surface of the parasite that play a major biological role in both insect and mammal-dwelling stages. Altogether, these studies confirm the complexity of T. cruzi genome revealing relevant concepts to better understand Chagas disease.

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Genome Sequence of Trypanosoma cruzi Strain Bug2148

Cited by 16 publications

References 12 publications

Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics

Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics

Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity

Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

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