An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley

Abstract Background The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The Qingke in China has about 3500 years of cultivation history, mainly produced in Tibet, Qinghai, Sichuan, Yunnan and other areas. In addition, Qingke has rich nutritional value and outstanding health effects, including the beta glucan, dietary fiber, amylopectin, the contents of trace elements, which are higher than any other cereal crops. Findings Here, we reported an improved high-quality assembly of Qingke genome with 4.0 Gb in size. We employed the falcon assembly package, scaffolding and error correction tools to finish improvement using PacBio long reads sequencing technology, with contig and scaffold N50 lengths of 1.563Mb and 4.006Mb, respectively, representing more continuous than the original Qingke genome nearly two orders of magnitude. We also reannotated the new assembly, and reported 61,303 stringent confident putative proteincoding genes, of which 40,457 is HC genes. We have developed a new Qingke genome database (QGD) to download and use friendly, as well as to better manage the information of the Qingke genetic resources. Conclusions The availability of new Qingke genome and annotations will take the genetics of Qingke to a new level and will greatly simplify the breeders effort. It will also enrich the granary of the Tibetan people.