Comparative analysis of the complete chloroplast genome of endemic Colchicum baytopiorum CD. BRICKELL


MORGİL GERÇEK H., Unlu O., BOZTAŞ K., TULUM I., ÖZ G.

Revista Brasileira de Botanica, 2024 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Publication Date: 2024
  • Doi Number: 10.1007/s40415-024-01021-y
  • Journal Name: Revista Brasileira de Botanica
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Agricultural & Environmental Science Database, BIOSIS, CAB Abstracts
  • Keywords: Colchicaceae, cpDNA, Endemism, Phylogenetic relationships
  • Istanbul University Affiliated: Yes

Abstract

The Colchicum baytopiorum CD. BRICKELL belongs to the Colchicaceae, is a near threatened (NT) species of deciduous arbor endemic to Turkey, a medicinal plant species which has commercial value due to the usage areas of colchicine it contains. Adding to its importance, this is the first report of the C. baytopiorum chloroplast (cp) genome. The interspecies comparative analyses within Colchicum species is beneficial for species authentication and phylogenetic analysis. We performed whole genome Illumina Hiseq2500 sequencing to obtain the chloroplast DNA (cpDNA) sequence of Colchicum baytopiorum CD Brickell. We also performed a comparative analysis with five chloroplast genomes of previously reported representative taxa from the Colchicaceae family. Our results showed that the C. baytopiorum cp genome is 158,019 bp long and has 37.1% GC content. The genome has a 97,477 bp long large single copy region, 16,570 bp long a small single copy region and 22,986 bp long two inverted repeat regions. Whole gene number was 135, protein–coding genes 86. The cp genome contains 8 rRNA and 38 tRNA genes. IR regions were compared across the cp genome of the C. baytopiorum with five representative taxa from the Colchicaceae family. The IRa and IRb region is determined 22.986 bp in the C. baytopiorum, it is determined as approximately 26.000–28.000 bp in the others. Additionally, 37 simple sequence repeats (SSRs) were detected in the C. baytopiorum cp genome. In this study, based on the Ka/Ks ratios, positive selection for the C. baytopiorum cp genome draws attention to the matK, ccsA and atpH cp genes. This study is important for the phylogenetic relationship of Colchicum species, the expansion of the gene pool of the population and the understanding of evolutionary steps.