The paper quantifies false duplications in genome assemblies of platypus, zebra finch, and Anna's hummingbird, showing they lead to overestimated gene family expansions.

Genome biology · Sep 27, 2022Peer-reviewedGenomics

False gene and chromosome losses affected by assembly and sequence errors

Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M. Phillippy, Olivier D. Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan M. D. Wood, Richard Michael Durbin, Giulio Formenti, Samara Brown, Lindsey J. Cantin, Claudio V. Mello, , Erich David Jarvis

The paper evaluates new vertebrate genome assemblies from the VGP against previous references, finding significant improvements in completeness and accuracy.

Genome biology · Sep 27, 2022Peer-reviewedGenomics

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis A. Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony D. Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa M. Komoroske, Tanya M. Lama, , Olivier D. Fedrigo

The paper benchmarks DNA preservation methods for long-read and long-range sequencing across vertebrates, finding that optimal methods vary by taxa, tissue, and application.

GigaScience · Jan 1, 2022Peer-reviewedGenomics

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier D. Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, , Erich David Jarvis

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

Genome biology · Apr 28, 2021Peer-reviewedGenomics