Ítem
Acceso Abierto
Comparative genomics of Giardia duodenalis sub-assemblage AI beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes
Título de la revista
Autores
Rodrigo de Paula Baptista
Matthew S. Tucker
Matthew J. Valente
Subodh K. Srivastava
Nadya Chehab, Alison Li
Jahangheer S. Shaik
Juan David Ramirez
Benjamin M. Rosenthal,Asis Khan
Archivos
Fecha
2024-12-01
Directores
ISSN de la revista
Título del volumen
Editor
Scientific Reports
Buscar en:
Métricas alternativas
Resumen
Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of > 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.
Abstract
Palabras clave
Long-read sequencing , Genome assembly , Giardia , Annotation , Ploidy , Synteny
