Aquatic Plant Genomics: Advances, Applications, and Prospects

Table 1

Summary of the genomics studies and technologies correlated to aquatic plant species discussed in the review.

Genomics studies	Species	Applications
Molecular markers
SSR	Sparganium emersum [8], Ruppia cirrhosa [9], Euryale ferox [10], Nymphoides peltata [11, 12]	Genetic diversity analysis
	Cabomba aquatic [18], Nelumbon ucifera [19]	Phylogenetic analysis
AFLP	Utricularia australis [13]	Genetic diversity analysis
	Nelumbon ucifera [19]	Phylogenetic analysis
	Potamogeton ×maëmetsiae [22], Potamogeton clystocarpus [23]	Germplasm identification
ISSR	Ranunculus nipponicus [14], Alternanthera philoxeroides [16], Euryale ferox [17]	Genetic structure
EST-SSR	Nymphoides peltata [15]	Genetic diversity and structure
RAPD	Alternanthera philoxeroides [16], Euryale ferox [17]	Genetic diversity
Nuclear, chloroplast, and mitochondrial markers	Hydrocharitaceae(family) [20]	Phylogenetic analysis
	Potamogeton ×maëmetsiae [22], Potamogeton clystocarpus [23]	Germplasm identification
Plastid markers	Veronica sect. Beccabunga [21]	Phylogenetic and taxonomic analysis
Comparative genomics
Interspecies comparative genomics	Utricularia gibba [24, 25]	Gene family classification and functional gene prediction; Adaptive molecular evolution analysis
	Spirodela [26]
	Phaeodactylum tricornutum [30]
Functional genomics
PCR approach	Hydrilla verticillata [31]	Identify elements necessary for C4 system
	Potamogeton [37]	Identify HSFA2 and its putative target gene CP-sHSP
	Ceratophyllum demersum [85]	Identify the role of CdPCS1 in biosynthesis of PC
	Lemna gibba [50]	Elucidate the molecular responses stimulated by excess copper exposure
Specific probes from 3-UTR	Lemna gibba [33]	Analyze the expression of the six rbcS genes in different organs
RACE	Sagittaria graminea [34]	Analyze two RCA genes(SGrca1 and SGrca2) expression pattern
Gene mining method	Eichhornia crassipes [51]	Isolate genes involving low-sulfur tolerance to understand the mechanism of high efficiency nutrient acquisition and utilization
Genome/transcriptome sequencing
Chloroplast genome	Nuphar advena [53], Najas flexilis [54], Elodea canadensis [55], Lemna minor [57], Utricularia foliosa [56], Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana [58]	Important source of genetic markers for phylogenetic analysis; Identify functional coding regions and sequence outside of coding regions; Chloroplast transformation for genetic engineering; Evolution of chloroplast genomes
Mitochondrial genome	Spirodela polyrhiza [60], Butomus umbellatus [61]	Study the evolution of monocot mitochondrial genomes
Whole genome	Spirodela polyrhiza [62]	Stimulate new insights into environmental adaptation, ecology, evolution, and plant development; Future bioenergy applications
	Nelumbo nucifera [63]	Study the evolutionary history of the genome and genes involved in relevant processes governing the unique features
	Lemna minor [64]	Understand the biological and molecular mechanisms in L. minor; Facilitate future genetically improvements and biomass production applications of duckweed species
Transcriptome	Utricularia vulgaris [65, 66]	Identify gene losses and duplications during the course of evolution; Study adaptations related to the environment and carnivorous habit and evolutionary processes responsible for considerable genome reduction
	Ranunculus bungei [67]	Study the molecular adaptive mechanism from terrestrial to aquatic habitats
	Nasturtium officinale [68], Oenanthe javanica [69]	Annotate function genes; Promote the studies of medicinal properties and corresponding pathways
MicroRNA	Nelumbo nucifera [70, 71]	Identify conserved microRNAs and their target genes