Kudoa genomes

This repository contains data associated with: Weber CC et al., Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution.

Genomic data

Some of the data are still making their way into public repositories. In the meantime, the assemblies are available here.

Public release

Species	ToLID	Biosample	Primary assembly	Alternate haplotype	Mitochondrion	Assembly method
Kudoa neothunni	jmKudNeot1	SAMEA115884706	PRJEB82086	PRJEB82087	see primary	hifiasm-meta
Kudoa sp. trachurus	jmKudSpea1	SAMEA116001081	PRJEB80899	PRJEB80900	PRJEB81409	read_VAE*, wtdbg2

*See: Weber CC (2024) Disentangling cobionts and contamination in long-read genomic data using sequence composition

Gene annotation

Annotations were produced with BRAKER3 using protein hints from free-living Cnidarians and K. iwatai, and are available here.

Additional information

Embedding tools used for assemblies

• https://github.com/CobiontID/HiC_network
• https://github.com/CobiontID/read_VAE

Identification of Kudoa ribosomal SSU

• https://github.com/CobiontID/MarkerScan