The phylogenetic analysis based on eight sequences identified in this study and 12 species RPPs gene in GenBank revealed that all eight sequences belong to tet(M) taxa, which is one of the most prevalent class of RPPs gene conferring antibiotic resistance.
Our bioinformatic analysis of the top 500 putative MrpC binding sites did not identify Motif 1, which was proposed previously based on six sequences in the mrpC promoter region to which MrpC bound [ 44].
Primers BuT2_F 5′ CAGTGCTGCCAACAWTTYGT 3′ and BuT2_R 5′ CASTGCTGCCAATTTAGCYA 3′ were designed based on three sequences: the canonical BuT2 element from D. buzzatii (AF368884.1), the BuT2 sequence located in the scf2_1100000004958 2664879-26680344 (scf1_Dwil) of D. willistoni genome, and the one located in the scaffold_3367: 3535-7555 (scf1_D.oj) of D. mojavensis genome.
PolyPhen-2 predicts variants as 'benign', 'possibly damaging', or 'probably damaging' based on eight sequence-based and three structure-based predictive features [ 35].
We define a distance metric between samples based on seven sequencing quality control metrics from Picard (http://broadinstitute.github.io/picard).github.io/picard
We thus devised an approach that was based on five sequence comparisons among the orthologous and paralogous pairs of sequences estimating d n and d s (fig. 1 C).
Our CNV calling pipeline (discussed further in the Supplementary Material) works as follows: We define a distance metric between samples based on seven sequencing quality control metrics from Picard (http://broadinstitute.github.io/picard ).github.io/picard
Its structure is based on two identical sequences derived from enkephalins joined C-terminal to C-terminal by an hydrazide bridge (Tyr-D-Ala-Gly-Phe-NH-NH ← Phe ← Gly ← D-Ala ← Tyr).
Degenerate primers were designed based on two conserved sequences found in HCS-like cassette of genes and from PKS pathways (forward primer 5'- CTNCCNTandAYGAYCCCGT-3' and reverse primer 5'-NCKRTGNGCNCCYTTNACCAT-3').
Based on two DNA sequences (nrDNA ITS and MAT1-2-1), significant genetic divergence was detected among 56 isolates of O. sinensis collected from different regions of the Tibetan Plateau.
