Complete Sequences Of Nelumbo Plastid Genome: Insights Into Sytematic Position Of Nelumbo

There are two surviving Nelumbo species now:Nelumbo nucifera Gaertn. and Nelumbo lutea Willd. Nelumbo was considered as a member of Nymphaeales (water lilies) for a long time, the systematic position of the genus Nelumbo has long remained unsettled. The genome research is essential to understand the systematic position of Nelumbo, and to improve the lotus breeding. We report the complete plastid genome sequences of the Nelumbo, the phylogence of Nelumbo was inferred and are discussed, and we sequensed the Nelumbo genome.The main results are as follows:1. We sequenced the two complete plastid genome sequences of N. lutea and N. nucifera using Shot-Gun sequencing. The sizes of the N. lutea and N. nucifera plastid genomes are 163,206 and 163,307 bp, respectively. The overall GC contents are 38.01%(N. lutea) and 37.99%(N. nucifera), similar to the currently available plastid genomes of stem dicots. The Nelumbo plastome contains 113 different genes, including four distinct rRNAs (16S,23S,4.5S and 5S),30 distinct tRNAs and 79 distinct peptide-coding genes. Four rRNA, seven tRNA and six peptide-coding genes (including rps12) are duplicated in the IR region, giving a total of 130 genes.55.66% of the plastid is covered by coding regions, including peptide-coding genes (79,086 bp; 48.43%), ribosomal RNA genes (9,026 bp; 5.53%) and transfer RNA genes (2,788bp; 1.71%). The remaining 44.34% consists of intergenic regions (58,078 bp; 35.56%) and introns (14,329 bp; 8.77%). We detected 398 SNP (single nucleotide polymorphism) sites and 161 INDEL (insert/delete) sites between the N. lutea and N nucifera plastid genomes.2. To resolve the long-standing controversies about the phylogeny of Nelumbo, we report here the two complete plastid genome sequences of N. lutea and N. nucifera. Simultaneously, a DNA matrix containing 78 protein-coding genes from four gymnosperms and 78 angiosperms was analyzed using three phylogenetic methods (maximum parsimony, MP; maximum likelihood, ML; and Bayesian inference, BI). The results implied that Nelumbo is a stem endicot and should be placed into the Proteales. Nelumbonaceae have an age of 110 million years, and the splitting between N. lutea and N. nucifera is estimated to have occurred about 2.41 Mya.3. We report the development and characterization of microsatellite primers designed for Nelumbo nucifera, Euryale ferox and Zizania latifolia.Using these polymorphic microsatellite markers, we select the ZJH wild lotus as the best sequencing material. We did the Nelumbo genome survey using about 18G sequencing data. The genome size of Nelumbo is about 879Mp and the heterozygous rate in this genome is very low. There are some repeat regions in this genome, according to the distribution of GC depth, we can infer that the GC content of Nelumbo genome is about 37%. This work will be useful in nelumbo linkge map constraction and physical map constraction.