Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains

Valdivia, H.O.; Gilman, Robert Hugh; Andersson, B.; Reis-Cunha, J.L.; Baptista, R.P.; Loss de Morais, G.; Guedes, R.; Talavera Lopez, C.; Macedo, A.M.; Bartholomeu, D.C.; Bern, C.; Vasconcelos, A.T.; Rodrigues-Luiz, G.F.; Mendes, T.A.O.

dc.contributor.author	Reis-Cunha, J.L.
dc.contributor.author	Rodrigues-Luiz, G.F.
dc.contributor.author	Valdivia, H.O.
dc.contributor.author	Baptista, R.P.
dc.contributor.author	Mendes, T.A.O.
dc.contributor.author	Loss de Morais, G.
dc.contributor.author	Guedes, R.
dc.contributor.author	Macedo, A.M.
dc.contributor.author	Bern, C.
dc.contributor.author	Gilman, Robert Hugh
dc.contributor.author	Talavera Lopez, C.
dc.contributor.author	Andersson, B.
dc.contributor.author	Vasconcelos, A.T.
dc.contributor.author	Bartholomeu, D.C.
dc.date.accessioned	2019-04-24T18:23:51Z
dc.date.available	2019-04-24T18:23:51Z
dc.date.issued	2015
dc.identifier.uri	https://hdl.handle.net/20.500.12866/6460
dc.description.abstract	Background: Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. CL Brener, the reference strain of the T. cruzi genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in T. cruzi. Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the T. cruzi karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different T. cruzi strains. Despite these studies, the extent of diversity in CCNV among T. cruzi strains based on a read depth coverage analysis has not been determined. Results: We identify the CCNV in T. cruzi strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in T. cruzi than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six T. cruzi samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival. Conclusions: Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.	en_US
dc.language.iso	eng
dc.publisher	BioMed Central
dc.relation.ispartofseries	BMC Genomics
dc.rights	info:eu-repo/semantics/restrictedAccess
dc.rights.uri	https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject	aneuploidy	en_US
dc.subject	Article	en_US
dc.subject	chromosome	en_US
dc.subject	chromosome 14	en_US
dc.subject	chromosome 31	en_US
dc.subject	chromosome 6	en_US
dc.subject	chromosome analysis	en_US
dc.subject	chromosome map	en_US
dc.subject	controlled study	en_US
dc.subject	copy number variation	en_US
dc.subject	discrete typing unit	en_US
dc.subject	gene dosage	en_US
dc.subject	gene frequency	en_US
dc.subject	gene ontology	en_US
dc.subject	genetic parameters	en_US
dc.subject	genetic variability	en_US
dc.subject	genome	en_US
dc.subject	genome plasticity	en_US
dc.subject	glycosylation	en_US
dc.subject	haplotype	en_US
dc.subject	heterozygosity	en_US
dc.subject	nonhuman	en_US
dc.subject	parasite examination	en_US
dc.subject	parasite survival	en_US
dc.subject	sequence analysis	en_US
dc.subject	single nucleotide polymorphism	en_US
dc.subject	strain difference	en_US
dc.subject	Trypanosoma cruzi	en_US
dc.subject	Y chromosome	en_US
dc.subject	Y chromosome 11	en_US
dc.subject	copy number variation	en_US
dc.subject	gene expression	en_US
dc.subject	genetic variation	en_US
dc.subject	genetics	en_US
dc.subject	genome	en_US
dc.subject	genomics	en_US
dc.subject	procedures	en_US
dc.subject	Trypanosoma cruzi	en_US
dc.subject	Trypanosoma cruzi	en_US
dc.subject	protozoal DNA	en_US
dc.subject	DNA Copy Number Variations	en_US
dc.subject	DNA, Protozoan	en_US
dc.subject	Gene Expression	en_US
dc.subject	Genetic Variation	en_US
dc.subject	Genome, Protozoan	en_US
dc.subject	Genomics	en_US
dc.subject	Glycosylation	en_US
dc.subject	Trypanosoma cruzi	en_US
dc.title	Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains	en_US
dc.type	info:eu-repo/semantics/article
dc.identifier.doi	https://doi.org/10.1186/s12864-015-1680-4
dc.subject.ocde	https://purl.org/pe-repo/ocde/ford#1.06.07
dc.relation.issn	1471-2164

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