Survivors from these families were identified, their genomic DNA was extracted (using the Qiagen DNeasy 96 protocol Blood & Tissue kit), and genotyped (by LGC Genomics Ltd) for the same sparse SNP panel used for parentage assignment of mortalities (Supplementary Table 2).
The chip used harbored 906,481 nDNA SNPs and 119 mtDNA SNPs, of which 28 were informative in our analyzed population for mtDNA haplogroup assignment in HaploGrep (supplementary table S2, Supplementary Material online) (Kloss-Brandstätter et al. 2011).
Using the same concatenated data set for 897 protein-coding sequences, a parsimonious analysis showed same assignment of strains into clades (supplementary fig. S1, Supplementary Material online).
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We used the macro-precision and macro-recall as measures of assignment performance (Supplementary Materials, 'Performance measures').
The macro-precision for the taxonomic assignment of 7176 16S rRNA genes (Supplementary Fig. S4) was constantly above 92% (Supplementary Fig. S3a) in the combined cross-validation (Methods), using the whole-genome reference sequences in mRefSeq47 (Supplementary Fig. S5), not just the 16S genes.
The 'reference dataset for COG (Cluster of Orthologous Groups of proteins) assignment' (Supplementary Table S2) contained 343 microbial genome sequences where COG assignment has been made for all the genes by the NCBI.
The highest and lowest loading values reflect the lipid species that are most important variable in the assignment of each principal component (Supplementary Sheet S4).
We extracted the top 20% DEGs in the Chinese alligator gonads and performed chromosomal assignment of the orthologs in humans (Supplementary information, Figure S10A) and chickens (Supplementary information, Figure S10B).
For a more detailed description of CNV assignment, see Supplementary Material.
A backbone assignment of 13C15N-UbcH5a was performed (see Supplementary Fig. S3) to identify the amino acids that underwent perturbations in the presence of RNF125stop129.
