Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid <i>Angomonas deanei</i>

Davey, John W.; Catta-Preta, Carolina Moura Costa; James, Sally; Forrester, Sarah; Motta, Maria Cristina M.; Ashton, Peter D.; Mottram, Jeremy C.

doi:10.1093/g3journal/jkaa018

Cited by 15 publications

(10 citation statements)

References 39 publications

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“…Assembled sequences were polished by Arrow 2.3.3 (Pacific Biosciences). The polished assembly was checked by Tapestry 1.0.0 ( Davey et al 2021 ) with default values. The telomeric repeat TTAGGG ( Cohn et al 2005 ) was for the detection of telomeric repeats.…”

Section: Methodsmentioning

confidence: 99%

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

Kashiwa

Suzuki

2021

G3 Genes|Genomes|Genetics

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Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices. Several Cercospora species can affect soybeans, such as C. kikuchii which causes soybean leaf blight. Speciation in Cercospora on soybean has not been adequately studied. Some cryptic groups of Cercospora also cause diseases on soybean. Moreover, it has been known C. kikuchii population genetic structure is different between countries. Consequently, further genomic information could help to elucidate the covert differentiation of Cercospora diseases in soybean. Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb. Based on ab-initio gene prediction, several pathogenicity-related genes, including 242 genes for effector candidates, 55 secondary metabolite gene clusters, and 399 carbohydrate-active enzyme genes were identified. The genome sequence and the features described in this study provide a solid foundation for comparative and evolutionary genomic analysis for Cercospora species that cause soybean diseases worldwide.

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Section: Methodsmentioning

confidence: 99%

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

Kashiwa

Suzuki

2021

G3 Genes|Genomes|Genetics

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“…Genomic or RNA-seq illumina reads were downloaded from the European Nucleotide Archive (ENA) ( A. deanei genome: PRJEB36170 [ 73 , 74 ], B. saltans RNA-seq: PRJEB3146 [ 75 , 76 ], E. monterogeii RNA-seq: PRJNA680236 [ 77 , 78 ], P. confusum poly(A)-enriched RNA-seq: PRJNA414522 (sample SAMN07793202) [ 79 , 80 ]). Reads were assessed for quality, trimmed, base calls corrected and adapter sequences removed using fastp [ 81 ] version 0.23.2 with the following flags: —detect_adapter_for_pe, —overrepresentation_analysis, —correction and —cut_right.…”

Section: Methodsmentioning

confidence: 99%

A lineage-specific protein network at the trypanosome nuclear envelope

Butterfield,

Obado,

Scutts

et al. 2024

Nucleus

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The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei , a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term l amina- a ssociated p roteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens , and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.

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“…Of these 83 genomes, 31 are from Leishmania and 43 are from Trypanosoma genera. TriTrypDB also has genomes of other parasitic kinetoplastids including, Angomonas deanei [ 11 ] , Blechomonas ayalai , Crithidia fasciculata [ 12 ] , Endotrypanum monterogeii [ 12 ] , Leptomonas pyrrhocoris [ 13 ] , Leptomonas seymouri [ 14 ] , Paratrypanosoma confusum [ 15 ], and Porcisia hertigi [ 16 , 17 ] and free-living nonparasitic kinetoplastid Bodo saltans . Gene annotations are available for 66 of these sequences, while the remaining 17 are genome assemblies without annotations ( Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

TriTrypDB: An integrated functional genomics resource for kinetoplastida

et al. 2023

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Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org). As of release 59, TriTrypDB hosts 83 kinetoplastid genomes, nine of which, including Trypanosoma brucei brucei TREU927, Trypanosoma cruzi CL Brener and Leishmania major Friedlin, undergo manual curation by integrating information from scientific publications, high-throughput assays and user submitted comments. TriTrypDB also integrates transcriptomic, proteomic, epigenomic, population-level and isolate data, functional information from genome-wide RNAi knock-down and fluorescent tagging, and results from automated bioinformatics analysis pipelines. TriTrypDB offers a user-friendly web interface embedded with a genome browser, search strategy system and bioinformatics tools to support custom in silico experiments that leverage integrated data. A Galaxy workspace enables users to analyze their private data (e.g., RNA-sequencing, variant calling, etc.) and explore their results privately in the context of publicly available information in the database. The recent addition of an annotation platform based on Apollo enables users to provide both functional and structural changes that will appear as ‘community annotations’ immediately and, pending curatorial review, will be integrated into the official genome annotation.

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Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

Cited by 15 publications

References 39 publications

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

A lineage-specific protein network at the trypanosome nuclear envelope

TriTrypDB: An integrated functional genomics resource for kinetoplastida

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