Genetic diversity of MHC and coccidial mitogenomes from fecal samples of the red‑crowned crane (Grus japonensis).

Non‑invasive fecal sampling coupled with molecular analysis is an established tool in avian research. Herein, we used this approach to investigate the polymorphism of the MHC IIB gene in Grus japonensis and obtained three complete coccidia mitochondrial genomes (mitogenomes) from fecal samples. We identified a total of 19 MHC IIB exon 2 alleles in 85 fecal samples, with 13 of them being newly discovered. All alleles had a length of 270 bp. The nucleotide diversity among the 19 alleles was 0.156, with 42 amino acid variation sites, and Grja-DAB*001 was identified as the common allele. The three complete coccidia mitogenomes had lengths of 6359 bp, 6335 bp, and 6226 bp, respectively, each containing three protein-coding genes (Cytb, COⅠ, and COⅢ). Phylogenetic analysis revealed that these three coccidia clustered separately with six coccidia from Grus nigricollis. Among 44 estimated individuals of G. japonensis, we detected coccidia in 20 individuals, resulting in an apparent prevalence rate estimates of 45.45%. We also observed mixed infections with multiple coccidia. The results provide host genetic diversity and parasite occurrence data for this species.