Analyzing genetic diversity of chloroplast genomes in Liliales

Abstract

Abstract
Liliales is a monocotyledonous order and contains both photosynthetic and
mycoheterotrophic species that distribute locally or worldwide. In this study, the
genetic diversity of chloroplast genomes in Liliales was explored regarding their
nucleotide diversity and repeated composition. The analysis of nucleotide diversity
revealed various hotspots in large and small single-copy regions whereas the IR regions
had low sequence divergence. Although each family has specific hotspots, the rps15-
ycf1 region was commonly found as a highly variable area in the cpDNA of observed
taxa. In the cpDNA of Liliales, mononucleotide simple sequence repeat (SSR) is the
most common type. The majority of SSRs are located in non-coding regions. Similarly,
more long repeats were found in non-coding areas than in coding sequences.
Additionally, the complement repeat exceeds forward type in the cpDNA of Liliales.
The highest number of long repeats was found in Corsia dispar whereas that of SSRs
was detected in Smilax china. The results of nucleotide diversity and repeat analyses
provided fundamental information for further studies on population genetics, molecular
marker development and evolutionary history of Liliales.
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