First complete chloroplast genome of the Indian endemic Anaphalis hookeri (Gnaphalieae, Asteraceae): Insights into genome structure and phylogenetic implications

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Anaphalis hookeri C.B. Clarke ex Hook.f. is a narrow endemic species from Eastern Himalayan region of Sikkim, India. In the present study, the complete chloroplast genome of A. hookeri was sequenced, assembled, and annotated. The genome exhibited a typical circular quadripartite structure with a length of 153,209 bp. The large single-copy region (84,945 bp) and small single copy region (18,498 bp) was separated by two inverted repeat regions (IRa and IRb: 24,883 bp). Total 132 genes were annotated, including 87 protein-coding genes, 37 transfer RNA and eight ribosomal RNA genes. Relative Synonymous Codon Usage analysis revealed a bias for codons ending in A or T. Amino acid frequency analysis showed that Leucine was the most encoded Amino acid, whereas Cysteine was the least frequent. We also identified 60 SSRs in the cp genome with mononucleotide repeats being the most prevalent followed by tetranucleotide repeats. Phylogenomic analysis based on 50 Anaphalis species and species from allied genera confirmed the placement of A. hookeri within the genus. The study contributes a novel chloroplast genome data which will provide valuable genetic information for future comparative genomics and phylogenetic studies within the genus.