Abstract
Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine rich in sesquiterpenes that has been widely used in China and Japan for the treatment of viral infections. Despite its important pharmacological value, genomic information regarding A. lancea is currently unavailable. In the present study, the whole genome sequence of A. lancea was obtained using an Illumina sequencing platform. The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome. Based on the genomic data of A. lancea, 27,582 simple sequence repeat (SSR) markers were identified. The differences in representation among nucleotide repeat types were large, e.g., the mononucleotide repeat type was the most abundant (54.74%) while the pentanucleotide repeats were the least abundant (0.10%), and sequence motifs GA/TC (31.17%) and TTC/GAA (7.23%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. A total of 93,434 genes matched known genes in common databases including 48,493 genes in the Gene Ontology (GO) database and 34,929 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This is the first report to sequence and characterize the whole genome of A. lancea and will provide a theoretical basis and reference for further genome-wide deep sequencing and SSR molecular marker development of A. lancea.
Highlights
Atractylodes lancea (Thunb.) DC., which belongs to the Asteraceae (Compositae) plant family, has been widely used as traditional medicine in many countries, including China and Japan
The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome
Fresh leaves at the apex of A. lancea plants were transported in liquid nitrogen to the laboratory where they were stored at −80 ◦C until needed in subsequent experiments
Summary
Atractylodes lancea (Thunb.) DC., which belongs to the Asteraceae (Compositae) plant family, has been widely used as traditional medicine in many countries, including China and Japan. The main pharmacologically active components of A. lancea are present in the volatile oils and include atractylon, atractylodin, hinesol and β-eudesmol [1,2]. A. lancea has immunomodulatory activity [7]. The chromosome number and karyotype of A. lancea have been studied. The chromosome number of A. lancea is 2n = 24, and the karyotype is 2B [8,9,10]. The genomes of Compositae plants, such as Carthamus tinctorius [15] and Artemisia annua [16], have been sequenced, and these genome studies can provide a reference for the development of these medicinal plants
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