Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress

Abstract

Water dropwort (Liyang Baiqin, Oenanthe javanica (BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing of O. javanica via HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research on O. javanica (database homepage: http://apiaceae.njau.edu.cn/waterdropwortdb). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship between O. javanica and Daucus carota was the closest. Twenty-five gene families of O. javanica were found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation in O. javanica under different water conditions were further investigated. Two miRNA and target gene pairs (miR408 and Oja15472, miR171 and Oja47040) were remarkably regulated by water stress. The obtained reference genome of O. javanica provides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of the O. javanica response to water stress, including morphological, anatomical, and genetic differentiation.

Changes in Carotenoid Concentration and Expression of Carotenoid Biosynthesis Genes in Daucus carota Taproots in Response to Increased Salinity

“…The carrot (Daucus Carota L.) is the most representative root vegetable of the Apiaceae family, which is grown all over the world [1,2]. Carotenoid accumulation in carrot taproots is a complex regulatory process.…”

Exogenous Melatonin Enhances Photosynthetic Capacity and Related Gene Expression in A Dose-Dependent Manner in the Tea Plant (Camellia sinensis (L.) Kuntze)

“…The effects of melatonin on the growth and development of tea plants need further study. With the further development of integrative omics analysis and deep genome sequencing of tea plants and other higher plants [ 4 , 47 , 48 , 49 , 50 ], new ideas and schemes will be provided for the effects of melatonin on photosynthetic characteristics and growth and development of tea plant and other higher plant.…”

Isolation and Characterization of an LBD Transcription Factor CsLBD39 from Tea Plant (Camellia sinensis) and Its Roles in Modulating Nitrate Content by Regulating Nitrate-Metabolism-Related Genes

“…Cytological observation was conducted according to the method described by Han with slightly modification [ 48 , 49 ]. The samples of leaves and stems are fixed and dehydrated, and then cut into slices with ultramicrotome (Leica, Weztlar, German).…”