Genome Survey Sequencing, Microsatellite Motif Identification and Complete Mitogenome of Turnix Suscitator – Novel Implications for Charadriiformes Phylogeny

Abstract

Turnix suscitator is a primitive genus in the highly diverse order of shore birds Charadriiformes. Information regarding the evolutionary history of T. suscitator is sparse and its taxonomic position within Charadriiformes order debated. Hence we generated whole genome short read sequences of T. suscitator, mined microsatellite markers and created comprehensive phylogeny with the retrieved mitogenome. A total of 34142524 reads were sequenced with an estimated genome size of 817 mb. SPAdes assembly consisted of 320761 total contigs and an estimated N50 value of 907 base pairs. Krait identified a total of 77028 microsatellite motifs covering 0.64% of the total sequences in the SPAdes assembly. The complete mitogenome of T. suscitator was 16,816 bp in length with an AT- richness of 56.7% comprising 13 PCGs, 2 rRNAs and 22 tRNAs. Codon usage analysis revealed PCGs of T. suscitator mitogenomes were more biased towards codons ending with nucleotide A. Ka/Ks ratio for the select mitogenomes was less than 1, indicating the presence of purifying selection with nad1 being the most conserved gene (Ka/Ks = 0.07). BI and ML trees reveal 4 major clades within Charadriiformes order, namely Turnici with Turnix as a genus, Lari, and Scolopaci with Charadrii as sister clades. Phylogenetic and relative divergence time analysis of T. suscitator mitogenome revealed Turnix is not a sub-group/clade of Scolopaci, Charadrii or Lari rather an independently diverged clade within Charadriiformes order. The unique CR gene order observed only in T. suscitator mitogenome also supports the fact that Turnix as a clade has diverged independently and in parallel with the other 3 major clades. Overall our results provide overwhelming evidence to support a novel topological position of Turnix within phylogeny of Charadriiformes. Further the whole genome sequence and genome wide microsatellites of T. suscitator developed in this study will facilitate future genomic/evolutionary studies of Turnix species.

Keywords: Whole-genome, SSR, Mitogenome, Turnix phylogeny, Charadriiformes