Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Abstract

BackgroundSacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.ResultsThe genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment.ConclusionsThe slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.

Polyploidy-associated genome modifications during land plant evolution

“…At least one more polyploidy event was identified along the branches leading to all eudicot lineages depicted except Vitis [30,58,93,95]. Three independent polyploidy events were proposed on the terminal branch to Musa acuminata [34].…”

“…This is somewhat in conflict with the other large gains, which usually accompanied one or more WGD events. The inconsistency could be due to the timing and nature of the gamma event, which may actually be two events that occurred in close proximity, very early in the evolutionary history of eudicots [93].…”

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

“…Like the SEP1-SQUA and SEP3-SFT tandems in Figure 4A, we found that the AGL6-TM3 tandem gene arrangement is widespread across angiosperms (Figures 4B and 4C; Supplemental Data Set 3). For example, there is one AGL6-TM3 tandem gene pair in A. trichopoda and two such tandems in N. nucifera likely due to the most recent WGD this species experienced (Ming et al, 2013;Wang et al, 2013) ( Figure 4C; Supplemental Data Set 3). In V. vinifera, we also found two AGL6-TM3 tandems ( Figure 4C; Supplemental Data Set 3) that likely originated from the g triplication after which one tandem lost its AGL6 locus.…”

Cloning and characterization of the UBC gene from lotus (Nelumbo nucifera)

“…Notably, its seeds can survive for thousands of years, making it the oldest viable seed for which an age has been directly determined (Priestley and Posthumus, 1982). To date, the entire genomic sequence of N. nucifera has been published (Ming et al, 2013); however, the UBC gene has not yet been reported. Therefore, in this study, the UBC gene was cloned and characterized in N. nucifera.…”