First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing

d’Avila-Levy, Claudia M.; Bearzatto, Bertrand; Ambroise, Jérôme; Helaers, Raphaël; Butenko, Anzhelika; Yurchenko, Vyacheslav; Morelli, Karina Alessandra; Santos, Helena Lúcia Carneiro; Brouillard, Pascal; Grellier, Philippe; Gala, Jean‐Luc; Vikkula, Miikka

doi:10.3390/tropicalmed5010025

Cited by 5 publications

(8 citation statements)

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“…The genome of V. ingenoplastis was reassembled de novo using different programs, resulting in its significant improvement from the previously published version [ 17 ]. The obtained assembly is 34.3 Mbp (in contrast to the original 35.3 Mbp, hereafter the data of the previous assembly are given in parentheses) in 241 scaffolds (340) with N 50 of 591 kb (376 kb) and the longest contig of 2.4 Mb (1.6 Mb).…”

Section: Resultsmentioning

confidence: 99%

“…Nevertheless, a critical difference between these two trypanosomatids is that V. ingenoplastis has increased its genome size by gene duplications, while Phytomonas spp. has done exactly the opposite [ 17 , 25 ].…”

Section: Discussionmentioning

confidence: 99%

“…The genome of V. ingenoplastis was reassembled using sequencing data reported previously [ 17 ] with MaSuRCA assembler v. 3.3.9 with the default settings, followed by two rounds of polishing using the assembler-associated Polca software [ 57 ]. This pipeline was not tested by us previously [ 17 ]. It resulted in a more contiguous assembly, which was used in the current study.…”

Section: Methodsmentioning

confidence: 99%

“…Metabolic pathways of Vickermania ingenoplastis were analyzed as described previously [ 28 , 65 ], using “all against all” BLASTp searches with an E-value cutoff of 10 −20 and previously published (but reassembled) genomic data [ 17 ]. In some cases, a stricter E-value cutoff of 10 −50 was used in order to distinguish between true orthologous proteins and more distant homologs, which are not necessarily functional orthologues.…”

Section: Methodsmentioning

confidence: 99%

“…All these biochemical observations were experimental. Armed with the recently obtained genomic data for this species [ 17 ], we reanalyzed the metabolic potential of V. ingenoplastis , explain some earlier contradictory observation and provide a coherent framework for its unique metabolism. In particular, we documented that V. ingenoplastis has lost genes coding for the subunits of the respiratory complexes III and IV, increased a number of genes involved in carbohydrate metabolism, and lost the capacity to oxidize fatty acids and a number of aromatic and branched amino acids.…”

Section: Introductionmentioning

confidence: 99%

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The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions

et al. 2021

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A recently redescribed two-flagellar trypanosomatid Vickermania ingenoplastis is insensitive to the classical inhibitors of respiration and thrives under anaerobic conditions. Using genomic and transcriptomic data, we analyzed its genes of the core metabolism and documented that subunits of the mitochondrial respiratory complexes III and IV are ablated, while those of complexes I, II, and V are all present, along with an alternative oxidase. This explains the previously reported conversion of glucose to acetate and succinate by aerobic fermentation. Glycolytic pyruvate is metabolized to acetate and ethanol by pyruvate dismutation, whereby a unique type of alcohol dehydrogenase (shared only with Phytomonas spp.) processes an excess of reducing equivalents formed under anaerobic conditions, leading to the formation of ethanol. Succinate (formed to maintain the glycosomal redox balance) is converted to propionate by a cyclic process involving three enzymes of the mitochondrial methyl-malonyl-CoA pathway, via a cyclic process, which results in the formation of additional ATP. The unusual structure of the V. ingenoplastis genome and its similarity with that of Phytomonas spp. imply their relatedness or convergent evolution. Nevertheless, a critical difference between these two trypanosomatids is that the former has significantly increased its genome size by gene duplications, while the latter streamlined its genome.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions

et al. 2021

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Missing microbial eukaryotes and misleading meta-omic conclusions

Krinos,

Brisbin,

et al. 2023

Preprint

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Meta-omics has become commonplace in the study of microbial eukaryotes. The explosion of available data has inspired large-scale analyses, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. However, genome and transcriptome databases are prone to misannotation biases, and meta-omic inventories may have no recoverable taxonomic annotation for more than half of assembled contigs or predicted proteins. Direct mapping solely to organisms of interest might introduce a problematic misattribution bias, while full databases can annotate any cataloged organism but may be imbalanced between taxa. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We argue that ongoing curation of genetic resources is critical in accurately annotating protists in situ in meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem. We show that taxonomic membership of sequence clusters demonstrates more accurate estimated community composition than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and database selection and evaluation is a critical part of correctly annotating protistan taxonomy in environmental datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the critical importance of both database completeness and curation in enabling accurate environmental interpretation.

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Análise genômica comparativa e evolutiva do genoma do monoxeno Blechomonas sp. TCC303E

Tantaleán¹

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Acima de tudo, agradeço ao meu Deus, por seu mistério infinito onde dia a dia nós cientistas trabalhamos para entendê-lo um pouco mais.A minha mãe Lila Tantalean Campos e minha irmã Leidy Yannina Calderon Tantalean por serem minha força e empolgação para ser melhor a cada dia e a esse amor infinito que nos une, e também agradeço a meu amor de pandemia (agora noiva) Samara Spagnolo Sousa por sua parceria e companhia que me faz sentir bem cada dia. Agradeço também ao meu melhor amigo Hachi, por todos os momentos de diversão e tristeza juntos e aquele amor incondicional que os cães têm por seus donos, descanse em paz meu amigo.Ao Prof. João Marcelo Pereira Alves, mais conhecido pelo "J" por abrir as portas de seu laboratório para mim, pela oportunidade de fazer parte do time Labo 40; pela paciência e a confiança depositada para o desenvolvimento deste trabalho.Ao pessoal do lab. 40, Percy Omar Túllume Vergara e Anderson Carvalho Morais, obrigado pelo apoio e das dicas neste trabalho de mestre e também pela sua amizade. A Guillermo Uceda Campos pelas conversas e apoio sobre diversos assuntos.À Universidade de São Paulo, às agências de fomento à pesquisa CAPES pelo apoio financeiro. E para você, que embora seu nome não esteja listado nestes agradecimentos, mais que também contribui de alguma forma ou outra no desenvolvimento deste projeto. Só tenho a agradecer a todos vocês, muito obrigado! RESUMO O conhecimento dos tripanossomatídeos vem principalmente dos heteroxenos que foram muito mais estudados por terem impactos negativos na sociedade, deixando o maior grupo de tripanossomatídeos (monoxenos) quase esquecido por muito tempo. No entanto, os monoxenos se tornaram relevantes recentemente por serem bons modelos para entender a origem do parasitismo e a evolução dos heteroxenos, devido a serem basais a todos os heteroxenos importantes e compartilharem características genéticas comuns, além de co-infectar os hospedeiros desses heteroxenos. Diante dessa necessidade, este estudo tem como objetivo caracterizar o genoma do monoxeno Blechomonas sp. TCC303E (Classe Kinetoplastea; subfamília Blechomonadinae) através de técnicas bioinformáticas para analisar aspectos genômicos e evolutivos desse organismo, expandindo assim a disponibilidade de dados genéticos deste gênero, que até agora tinha disponível apenas a sequência genômica da espécie-tipo, Blechomonas ayalai. Blechomomas são parasitas extremamente polimórficos e exclusivos das pulgas (Siphonaptera), as quais podem transmitir agentes etiológicos de doenças veterinárias e médicas. Nossos resultados mostram uma montagem com uma cobertura média de 38,6 vezes, de boa qualidade e composta de 728 scaffolds, com N50 de ~61 kbp e uma média de GC de 50,3%. Um dos scaffolds contém DNA mitocondrial, com uma média de GC de 19,7%. Foram preditos 8.044 CDS, das quais foram anotadas funcionalmente 7.002, além de genes de RNAs: 71 tRNAs, 4 rRNAs, 62 RNAs não codificantes. A análise de sintenia mostrou que Blechomonas mantém uma arquitetura genômica semelhante à dos demais tripanossomat...

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First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing

Abstract: Here, we present first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis. This parasite was isolated repeatedly in the black blowfly, Phormia regina, and it forms a phylogenetically distinct clade in the Trypanosomatidae family.

Cited by 5 publications

References 23 publications

The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions

The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions

Missing microbial eukaryotes and misleading meta-omic conclusions

Análise genômica comparativa e evolutiva do genoma do monoxeno Blechomonas sp. TCC303E

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