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Attempts to establish the beautiful native American lotus in new locations have often been marked by failure, a fact which evokes scientific interest in the growth and dormancy habits of this plant. In spite of the fact that embryos have been known to sprout after two hundred years of dormany (6), it is doubtful if the plant reproduces from seed at all frequently in nature. The facile multiplication of tubers and the rapid growth of shoots from these create a competition for light and space which seedling's, if started under natural conditions, could probably not overcome. With the lotus in nature primarily dependent upon tubers for perpetuation, it is not surprising that florists in commercial production also rely chiefly upon them rather than upon seeds. The tubers produce a large flowering plant in a single season while the seedlings require at least two and sometimes probably as many as four years for floral development. No record has been found in the literature of successfully growing the plant from seed. It is stated (3) that if holes are made in the fruits and they are then placed in a pond, their embryos are so delicate that they do not survive. In another case no signs of plants were found a few years subsequent to the planting of thousands of the fruits sown just as they came from the pods (3). The writer is personally acquainted with men who have had similar failures. Scientifically, interest has centered largely in the germination of Nelumbo seeds. Old Indian lotus fruits obtained by Ohga from a prehistoric peat bed in South Manchuria are the most striking examples of protracted dormancy known to science (6). These were estimated to be three hundred to four hundred years old and certainly not less than two hundred years. A long period of dormancy has not been recorded for the American species but the fruit structure of the two species is practically alike and no sign of swelling occurs in either after being kept in water for several months (2). Ohga (6) found concentrated sulphuric acid treatment to be the easiest method of overcoming this dormancy. Fifty per cent, chromic acid and concentrated potassium hydrate also overcome the impermeability after a longer period of time. According to his work, practically all of the fruit coat shows the cellulose reaction. Shaw (9) describes the cells as having a middle lamella of a mixture of pectic compounds and lignin, and a cellu

WHEN we find a genus which is monotvpie in the existing flora, or one which contains but two or three geographically remote species, we may rest assured that the genus in question had anl interesting geological history and that its living representatives bn it z1 g e s ai are relicts of a day when the genus was widespread and (lomiflant. Notable examples, such as Liriodendron, Sequoia, and Nelumbo, may be cited. Comptonia is no exception to this rule. The single living species is confined to eastern North America, ranging as a lOIN shrub from Nova Scotia to \Manitoba and southward to North Carolina, Indiana, and Tennessee, while the number of ancient forms that have been described, is upwards of three score and amply proves the cosmopolitan character of the genus during the Tertiary periocl. Recent paleobotanists refer them as a, subgenus to \IMyrica, as is done in case of the living species by Engler (lNat i~ricehea Pflamzealjailiene, vol. 2, pt. 1, p. 28, 1889). MINoderni usage in this country, however, gives Comptonia generic rank, quite rightly so it seems to me. The space of a generation has passed since Schimper's classic Tra ie (le Paleontologie T %'letale sought to unify paleobotany)T, and the chaos of described species is even greater to-day than it was previous to 1870. Paleobotany is surely far enough advanced, it seems to me, for a more philosophical treatment, and while this little essay makes no pretension at embodying such a treatment, it is hoped that it will furnish the material that will be useful for that purpose when the proper time arrives. It is obvious enough to most botanists that existing species vary in their leaf characters through verv wide limits. I have had considerable to say about the leaf variation, atavistic ancl otherwise

Background The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as ‘SMRT (Single Molecule, Real-Time) sequencing’, has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. Results The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. Conclusions Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate ‘finished’ genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0289-0) contains supplementary material, which is available to authorized users.

Background MicroRNAs (miRNAs) play important roles in plant growth and development. MiRNAs and their targets have been widely studied in model plants, but limited knowledge is available concerning this small RNA population and their targets in sacred lotus (Nelumbo nucifera Gaertn.). Results In this study, a total of 145 known miRNAs belonging to 47 families and 78 novel miRNAs were identified during seed germination using high-throughput small RNA sequencing. Furthermore, some miRNA families which have not yet been reported in monocot or eudicot species were detected in N. nucifera, indicating that these miRNAs was divergence from monocots and core eudicots during evolution. Using degradome sequencing, 2580 targets were detected for all the miRNAs. GO (Gene Ontology) and KEGG pathway analyses showed that many target genes enriched in “regulation of transcription” and involved in “carbohydrate”, “amino acid and energy metabolism”. Nine miRNAs and three corresponding targets of them were further validated by quantitative RT-PCR. Conclusions The results present here suggested that many miRNAs were involved in the regulation of seed germination of sacred lotus, providing a foundation for future studies of sacred lotus seed longevity. Comparative analysis of miRNAs from different plants also provided insight into the evolutionary gains and losses of miRNAs in plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3032-4) contains supplementary material, which is available to authorized users.

Background The sacred lotus (Nelumbo nucifera) is widely cultivated in China for its edible rhizomes and seeds. Traditional plant breeding methods have been used to breed cultivars with increased yields and quality of rhizomes and seeds with limited success. Currently, the available genetic maps and molecular markers in lotus are too limited to be useful for molecular genetics based breeding programs. However, the development of next-generation sequencing (NGS) technologies has enabled large-scale identification of single-nucleotide polymorphisms (SNPs) for genetic map construction. In this study, we constructed an SNP-based high-density genetic map for cultivated lotus using double digest restriction site-associated DNA sequencing (ddRADseq). Results An F2 population of 96 individuals was derived from a cross between the rhizome lotus cultivar ‘Juwuba’ (male parent) and the seed lotus cultivar ‘Mantianxing’ (female parent). Genomic DNAs from this population were digested with the restriction enzymes EcoRI and MspI and then sequenced. In total, 133.65 Gb of raw data containing 1,088,935,610 pair-end reads were obtained. The coverage of reads on a reference genome was 7.2 % for the female parent, 6.56 % for the male parent, and 1.46 % for F2 individuals. From these reads, 10,753 valid SNP markers were used for genetic map construction. Finally, 791 bin markers (so-segregated adjacent SNPs treated as a bin marker), consisting of 8,971 SNP markers, were sorted into 8 linkage groups (LGs) that spanned 581.3 cM, with an average marker interval of 0.74 cM. A total of 809 genome sequence scaffolds, covering about 565.9 cM of the wild sacred lotus genome, were anchored on the genetic map, accounting for 70.6 % of the genome assembly. Conclusions This study reports the large-scale discovery of SNPs between cultivars of rhizome and seed lotus using a ddRADseq library combined with NGS. These SNPs have been used to construct the first high-density genetic map for cultivated lotus that can serve as a genomic reference and will facilitate genetic mapping of important traits in the parental cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2781-4) contains supplementary material, which is available to authorized users.

The response of macroinvertebrates to the progressive decomposition of the American lotus Nelumbo lutea (Willd.) Pers. was examined. Macroinvertebrate densities increased significantly with the onset and progressive senescence of the leaves, as reflected by decreasing chlorophyll a concentrations. The chironomid Polypedilum nymphaeorum Maschwitz and three species of Naididae exhibited positive responses to presumably increasing levels of food as leaf decomposition progressed. P. nymphaeorum larvae probably switched from feeding on periphyton to utilization of decomposing plant tissue and associated microbial decomposers once the Nelumbo leaves began to decompose. Naididae did not become abundant on the leaves until the onset of initial leaf decomposition. Densities of the carnivorous chironomid Ablabesmyia philosphagnos Beck and Beck were more closely related to the age of the leaves than to prey availability, older leaves having been colonized by several generations of individuals while the younger leaves had been colonized by only one

An in-depth study of the insects associated with the transfer of pollen in the American lotus was undertaken in a selected population on the Upper Mississippi River near La Crosse, Wisconsin. The study showed that members of the Coleoptera (Coleomegilla fascilabris Malsant, Diabrotica unidecimpunctata howardi Barber, D. virgifera Lec.), Diptera (Eristalis tenax (L.), Parhelophilus laetus (Locw)) and Hymenoptera (Agapostemon radiatus (Say), Apis mellifera L., Dialictus sp., Lasioglossum zonulum (Smith)) were the principal visitors and most obvious vectors in pollination. Although there are features of the flowers of the lotus that indicate cantharophily, such as the diurnal movements of the tepals and the food bodies of the anthers, in the area of study no special beetle-pollination system, as reported for such genera as Magnolia and Nuphar, appears to occur.

Small (1933) in his "Manual of the Southeastern Flora" designated the American or yellow lotus as Nelumbo lutea (Willd.) Pers. Synonyms include Nelumbium luteutm Willd., Nelumbo lutea Pers., Nelumbium pentapetalum Walt., Nelumbo pentapetala, and Nelumbium codophyllum Raf. The latter name was given 'by Robin (1817) to the lotus plants in Louisiana which were said to be much larger than those of Nelumbium luteunt. Examination of lotus colonies in Louisiana suggests that the larger size is to be attributed to the richer soils and longer growing season. The concensus among botanists seems to be that there is only one species of native lotus in America.

Background Lotus is a diploid plant with agricultural, medicinal, and ecological significance. Genetic linkage maps are fundamental resources for genome and genetic study, and also provide molecular markers for breeding in agriculturally important species. Genotyping by sequencing revolutionized genetic mapping, the restriction-site associated DNA sequencing (RADseq) allowed rapid discovery of thousands of SNPs markers, and a crucial aspect of the sequence based mapping strategy is the reference sequences used for marker identification. Results We assessed the effectiveness of linkage mapping using three types of references for scoring markers: the unmasked genome, repeat masked genome, and gene models. Overall, the repeat masked genome produced the optimal genetic maps. A high-density genetic map of American lotus was constructed using an F1 population derived from a cross between Nelumbo nucifera ‘China Antique’ and N. lutea ‘AL1’. A total of 4,098 RADseq markers were used to construct the American lotus ‘AL1’ genetic map, and 147 markers were used to construct the Chinese lotus ‘China Antique’ genetic map. The American lotus map has 9 linkage groups, and spans 494.3 cM, with an average distance of 0.7 cM between adjacent markers. The American lotus map was used to anchor scaffold sequences in the N. nucifera ‘China Antique’ draft genome. 3,603 RADseq markers anchored 234 individual scaffold sequences into 9 megascaffolds spanning 67% of the 804 Mb draft genome. Conclusions Among the unmasked genome, repeat masked genome and gene models, the optimal reference sequences to call RADseq markers for map construction is repeat masked genome. This high density genetic map is a valuable resource for genomic research and crop improvement in lotus.

Background Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the production of secondary metabolites. This enzyme has been identified in many organisms, ranging from prokaryotes to higher plants. Because Nelumbo nucifera is a basal dicot rich in many secondary metabolites, it is a suitable candidate for research on the phenylpropanoid pathway. Results Three PAL members, NnPAL1, NnPAL2 and NnPAL3, have been identified in N. nucifera using genome-wide analysis. NnPAL1 contains two introns; however, both NnPAL2 and NnPAL3 have only one intron. Molecular and evolutionary analysis of NnPAL1 confirms that it is an ancient PAL member of the angiosperms and may have a different origin. However, PAL clusters, except NnPAL1, are monophyletic after the split between dicots and monocots. These observations suggest that duplication events remain an important occurrence in the evolution of the PAL gene family. Molecular assays demonstrate that the mRNA of the NnPAL1 gene is 2343 bp in size and encodes a 717 amino acid polypeptide. The optimal pH and temperature of the recombinant NnPAL1 protein are 9.0 and 55°C, respectively. The NnPAL1 protein retains both PAL and weak TAL catalytic activities with Km values of 1.07 mM for L-phenylalanine and 3.43 mM for L-tyrosine, respectively. Cis-elements response to environmental stress are identified and confirmed using real-time PCR for treatments with abscisic acid (ABA), indoleacetic acid (IAA), ultraviolet light, Neurospora crassa (fungi) and drought. Conclusions We conclude that the angiosperm PAL genes are not derived from a single gene in an ancestral angiosperm genome; therefore, there may be another ancestral duplication and vertical inheritance from the gymnosperms. The different evolutionary histories for PAL genes in angiosperms suggest different mechanisms of functional regulation. The expression patterns of NnPAL1 in response to stress may be necessary for the survival of N. nucifera since the Cretaceous Period. The discovery and characterisation of the ancient NnPAL1 help to elucidate PAL evolution in angiosperms.

Background Nelumbo nucifera, known as sacred lotus, is a well-known medicinal plant and this lotus root is commonly used as food compared to different parts of this plant. This study was conducted to investigate the antioxidant and hepatic protective effects of lotus root hot water extract with taurine supplementation in high fat diet-induced obese rats. Methods Thirty-two male Sprague-Dawley rats (4-week-old) were randomly divided into four groups (n=8) for 6 weeks (normal diet, N group; high fat diet, HF group; high fat diet + lotus root hot water extract, HFR group; high fat diet + lotus root hot water extract + taurine, HFRT group). Lotus root hot water extract was orally administrated (400mg/kg/day) to HFR and HFRT groups and the same amount of distilled water was orally administered to N and HF groups. Taurine was supplemented by dissolving in feed water (3% w/v). Results The activities of glutamate oxaloacetate transaminase and glutamate pyruvate transaminase in serum were lower in HFR and HFRT groups compared to HF group. Thiobarbituric acid reactive substance contents in all groups fed a high fat diet were higher compared to N group. The activities of hepatic antioxidant enzymes were higher in HFR and HFRT groups compared to HF group. Conclusions These results suggest that lotus root hot water extract with taurine supplementation shows antioxidant and hepatic protective effects in high fat diet-induced obese rats.