MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Journal article

The Tyrrhenian tree frog (Hyla sarda) is a small cryptically coloured amphibian found in Corsica, Sardinia, and the Tuscan Archipelago. Investigation into the species’ evolutionary history has revealed phenotypic changes triggered by glaciation-induced range expansion, but understanding the genetic basis of this trait variation has been hampered by the lack of a reference genome. To address this, we assembled a chromosome-level genome of Hyla sarda using PacBio HiFi long reads, Bionano optical maps, and Hi-C data. The assembly comprises 13 assembled chromosomes, spanning a total length of 4.15 Gb with a scaffold N50 of 385 Mb, a BUSCO completeness of 94.60%, and a k-mer completeness of 98.30%. Approximately 75% of the genome consists of repetitive elements. We annotated 22,847 protein-coding genes with a BUSCO completeness of 94.60% and an OMArk completeness of 93.74%. This high-quality assembly provides a valuable resource for studying phenotypic evolution and its genomic basis during range expansion, and will assist future investigations into the population and conservation genomics of Hyla sarda

Authors: Uliano-Silva, M; Ferreira, JGRN; Krasheninnikova, K; Formenti, G; Abueg, L

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: BioMed Central
• Journal: BMC Bioinformatics
• Volume: 24
• Issue: 1
• Pages: 288-288
• Article number: 288
• Publication date: 2023-07-18
• DOI: 10.1186/s12859-023-05385-y
• EISSN: 1471-2105
• ISSN: 1471-2105
• Language: English
• Keywords: Genome; Perl; Phylogenetic tree; Computer science; Sequence assembly; Mitochondrial DNA; Biology; Genetics; Gene; Computational biology; Genome project