RT Journal Article
SR Electronic
T1 An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 409136
DO 10.1101/409136
A1 Xingquan Zeng
A1 Xiangfeng Li
A1 Lijun Bai
A1 Yulin Wang
A1 Tong Xu
A1 Hongjun Yuan
A1 Qijun Xu
A1 Sang Zha
A1 Zexiu Wei
A1 Wangmu Qimei
A1 Yuzhen Basang
A1 Jiabu Dunzhu
A1 Mingzai Yu
A1 Tashi Nyima
YR 2018
UL http://biorxiv.org/content/early/2018/09/07/409136.abstract
AB 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.BLASTBasic Local Alignment Search ToolBUSCOBenchmarking Universal Single-Copy OrthologsQVquality valuePacBioPacifc BiosciencesRNA-seqRNA sequencingNGSNext generation sequencingTGSThird generation sequencingQGDQingke Genome Database