De novo genome assembly of Myricaria laxiflora provides insights into its molecular mechanisms under flooding stress

Abstract

M. laxiflora is an endangered plant distributed in the Yangtze River floodplain of China, which often suffers from flood hazards during its growth and development. Due to the lack of a reference genome for M. laxiflora, the molecular regulatory mechanism of its waterlogging stress remains unclear. Here, we report for the first time the high-quality reference genome of M. laxiflora by using HiFi sequencing and Hi-C. The total assembly size of the M. laxiflora genome was 1.29 Gb with a scaffold N50 size of 29.5 Mb. A total of 23,666 genes encoding proteins and 5,457 ncRNA were predicted in this reference genome. In the M. laxiflora genome, a total of 101 MylAP2/ERF genes were identified and divided into 5 subgroups. Many MeJA responsive elements, ABA responsive elements, and hypoxia responsive elements were found in the promoter regions of these MylAP2/ERF genes. Based on transcriptome data analysis, a total of 74 MylAP2/ERF genes can respond to flooding stress. Meanwhile, it was found that three genes (MylAP2/ERF49/78/91) which belong to the same branch with RAP2.2 gene exhibited different expression trends under flooding stress. Our results provide valuable information on the molecular regulatory mechanism of flooding stress in M. laxiflora.