Tropical Plant Biology

Shen-Miller, J.; Aung, Louis; Turek, Jeff; Schopf, J.; Tholandi, Maya; Yang, Mei; Czaja, Andrew

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9125-1

During the Sino-Japanese conflict of the 1920s, Japanese botanist Ichiro Ohga was presented single-seeded fruit of Nelumbo nucifera var. China Antique collected by a local farmer from a dry lakebed in Northeast China (then, “Manchuria”). Ohga studied the fruit and published his findings. Years later, we tested the germination of Nelumbo fruit from the same locality. The oldest seed sprouted, having a germination time of ~3 days, was radiocarbon dated to be ~1300 years old. These cold- and drought-tolerant seeds exhibited shoot-before-root emergence and a primary green plumule capable of “dim-light” photosynthesis. Such traits and the notable long-term viability of the fruit spurred the interest of Ray Ming, University of Illinois that has now led to the sequencing of the Nelumbo genome. Analyses of this genome may provide insight into the biochemistry of Nelumbo on wax-biosynthesis genes, and application of aging-related thermostable proteins to the extension of seed-life and improvement of food quality of economic crops. Here, we review the history of these long-lived Nelumbo fruit, and their occurrence, discovery, collection, propagation, and methods of seedling care. The robust impermeable wax- and suberin-covered pericarp is a major factor contributing to their remarkable longevity. New findings are presented on the modern and 459- and 464-year-old pericarp anatomy, impermeability to water, and whole fruit and pericarp mechanical properties, and comparison of the mode of fruit weight-gain during imbibition and germination time relative to fruit maturity.

Shen-Miller, J.; Lindner, Petra; Xie, Yongming; Villa, Sarah; Wooding, Kerry; Clarke, Steven; Loo, Rachel; Loo, Joseph

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9124-2pmid: 24363819

Single-seeded fruit of the sacred lotus Nelumbo nucifera Gaertn var. China Antique from NE China have been shown to remain viable for as long as ~1,300 years, determined by direct radiocarbon-dating, and to have a germination rate of 84 %. The pericarp, a fruit tissue that encloses the single seeds of Nelumbo, is one of the major factors contributing to fruit longevity. Proteins that are heat stable and have a protective function are equally important to such centuries-long seed viability. We document proteins of Nelumbo fruit that are able to withstand heating, 32 % of which remained soluble in the 110 °C-treated embryo axis of a 549-year-old fruit and 76 % retained fluidity in its cotyledons. The genome of Nelumbo has recently been published and annotated. The amino-acid sequences of 11 “thermal proteins” (soluble at 100 °C) of modern Nelumbo embryo axes and cotyledons, identified by mass spectrometry, Western blot and bioassay, are assembled and aligned with those of an archaeal hyperthermophile Methancaldococcus jannaschii (“Mj,” an anaerobic methanogen having a growth optimum of 85 °C) and with those of five mesophile angiosperms. These thermal proteins have roles in protection and repair under stress. More than half (55 %) of the durable Nelumbo thermal proteins are present in the archaean Mj, indicating their ancient history. One Nelumbo protein-repair enzyme exhibits activity at 100 °C, having a heat-tolerance higher than the comparable enzyme of Arabidopsis. A list of 30 sequenced but unassembled thermal proteins of Nelumbo is appended.

Singh, Ratnesh; Ming, Ray; Yu, Qingyi

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9123-3

Nucleotide composition of genomes varies among organisms and among genes within a genome. Knowing the variations of nucleotide composition and the consequences of these differences would provide fundamental information for understanding genome evolution. Lotus (Nelumbo nucifera Gaertn.), a basal eudicot, diverged from its closest sister lineage at 135–125 MYA. The unique phylogenetic position of lotus makes it important for evolutionary studies. With the draft genome sequence of lotus available, we analyzed the nucleotide composition of the lotus genome compared to other sequenced plant genomes. GC content of the lotus genome was between grasses and eudicots. The lotus genome had more coding sequences with high GC3 than did the core eudicots, and its GC3 composition exhibited a negative gradient along the transcription direction. The difference between purines and pyrimidines in the coding sequence of lotus was smallest among the selected eudicot species. The lotus genome had a lower observed/expected (O/E) ratio of CpG dinucleotide than did the selected dicots and monocots except for grape. The lower O/E ratio of CpG dinucleotide is likely caused by instability of transposable elements, rather than a higher mutation rate.

Jia, Rui; Ming, Ray; Zhu, Yun

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9122-4

Nucleotide-binding site (NBS) containing genes comprise the largest class in identified plant resistance genes. A total of 137 NBS class resistance genes were identified from the newly sequenced sacred lotus genome (Nelumbo nucifera Gaertn.) through a reiterative computational sequence analysis. Three distinct groups of NBS-encoding genes were classified: 5 with Toll/interleukin-1 receptor homology (TIR) domain at N-terminal (TIR-NBS [-LRR (leucine-rich repeat)]), 37 with CC (coiled coil) domain (CC-NBS [-LRR]), and 95 with neither TIR nor CC at N-terminal (NBS [-LRR]). Sequence analysis revealed high divergence of NBS-LRR genes in sacred lotus. The result of cluster and syntenic analysis of NBS genes suggested a duplication and recombination event, which is consistent with the correspondent result of whole genome analysis. In addition, we also identified 52 NBS genes which have a putative NACHT domain embedded in the NBS domains. This characteristic has only been reported in animals, fungi and bacteria, suggesting that NACHT and NBS domains shared a similar ancient origin; and sacred lotus NBS (NACHT) genes may represent a transition role during the early evolution of disease resistance in land plants.

Zheng, Yun; Jagadeeswaran, Guru; Gowdu, Kanchana; Wang, Nian; Li, Shaohua; Ming, Ray; Sunkar, Ramanjulu

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9127-z

MicroRNAs (miRNAs) are small non-coding regulatory RNAs that degrade or repress protein synthesis of their messenger RNA targets. This mode of posttranscriptional gene regulation is critical for plant growth and development as well as adaptation to stress conditions. Sacred lotus (Nelumbo nucifera) is a land plant but adapted to the aquatic environment. It is a basal eudicot in the order Proteales, with significant taxonomic importance. Thus identification of miRNAs in sacred lotus could provide information about miRNA evolution, particularly the conservation as well as divergence of miRNAs in dicots. To identify conserved and novel miRNAs in sacred lotus, small RNA libraries from leaves and flowers were sequenced as well as computational strategy was employed. These approaches resulted in identification of 81 miRNAs that can be grouped into 41 conserved/known miRNA families and 52 novel miRNAs forming 49 novel miRNA families. Using 3 mismatches between miRNAs and their mRNA targets as cutoff, we have predicted 137 genes as targets for the conserved and known miRNAs. Overall, this analysis provided a glimpse of miRNA-dependent posttranscriptional gene regulations in sacred lotus.

Lum, Gengkon; VanBuren, Robert; Ming, Ray; Min, Xiang

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9121-5

Sacred lotus, Nelumbo nucifera (Gaertn.), is a basal eudicot with agricultural and medicinal importance. The secretome and proteins in some other subcellular locations including endoplasmic reticulum (ER), mitochondrion, chloroplast, and membrane of sacred lotus were predicted using a set of computational tools. The distribution of proteins in each subcellular location in sacred lotus was compared with proteins in five other plant species. Plant proteomes contained approximately 6–9 % of secreted proteins, 13–15 % membrane proteins, 12–20 % mitochondrial or chloroplast proteins, respectively. Plant secreted proteins consist of a large number of hydrolases and peroxidases which may contribute to cell wall formation, rhizome development and seed germination regulation. The information of secretome and other protein subcellular locations in sacred lotus and other species can be accessed at the PlantSecKB website ( http://proteomics.ysu.edu/secretomes/plant.php ).

Nelson, David; Schuler, Mary

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9119-z

Cytochrome P450 monooxygenases (P450s) in the sacred lotus (Nelumbo nucifera) genome have been identified and named according to systematic P450 nomenclatures. Comparisons of these sequences with those in the papaya and grape CYPomes have indicated that gene blooms exist in the CYP89, CYP94, CYP96 and CYP714 families and that less dramatic expansions exist in the CYP71 and CYP72 families. Expansions in the CYP94 and CYP96 families may be associated with generation of the extremely hydrophobic leaf surfaces associated with the “lotus effect” in this water-adapted species, since these families are known to hydroxylate fatty acids and alkanes in the wax biosynthetic pathways of other plant species. Evolution of the CYP719 and CYP80 families may be associated with production of a number of benzylisoquinoline and aporphine alkaloids. Structures for anonaine and roemerine, two of the most abundant aporphine alkaloids in lotus leaves and seeds, contain methylenedioxy bridges that are known to be generated by members of the CYP719 family. With only one CYP719A22 gene existing in the lotus genome, it is likely that it is involved in making aporphine alkaloids. The fact that CYP719 has not previously been seen in angiosperm phylogeny below the order of Ranunculales suggests that its presence in lotus (in the Proteales) presents an evolutionary terminus prior to its loss in more recent eudicot species. With several CYP80 family genes existing in the lotus genome, there are multiple candidates for those involved in conducting benzylisoquinoline alkaloid synthesis.

Paull, Robert; Carroll, Andrew; Chen, Nancy

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9129-x

The lotus genome (Nelumbo nucifera (Gaertn.)) lacks the paleo-triplication found in other eudicots and has evolved remarkably slowly with fewer nucleotide mutations. It is thought to have greater retention of duplicated genes than other angiosperms. We evaluated the potential genes involved in cell wall synthesis and its modification, and ethylene synthesis and response. In many cell wall transferases and hydrolases families, lotus had fewer members in most families when compared to Arabidopsis. Lotus had similar or fewer members in each family as found in poplar, grape and papaya. The exceptions were in the sialyl and beta-glucuronsyl transferases where similar number were found as in the core eudicots. Lotus had similar numbers of polygalacturonase and pectin methyl esterases as found in Arabidopsis but fewer in all other hydrolases families. For starch degradation, lotus had only two alpha amylases predicted genes versus eight to ten in other eudicots, with similar numbers of beta amylase genes predicted. Lotus also had less than half the number of genes predicted for the enzymes involved in lignin and tannin synthesis compared to Arabidopsis. The stress plant growth regulator ethylene’s synthesis, reception and response predicted genes were fewer in lotus than other eudicots. Only two ethylene receptor genes were predicted in lotus with five reported for Arabidopsis and six for tomato. Our analysis does not supports the conclusion that this species has greater retention of duplicated genes though our data does support the conclusion that lotus split occurred at the base of the eudicots.

Kim, Min-Jeong; Nelson, William; Soderlund, Carol; Gang, David

2013 Tropical Plant Biology

doi: 10.1007/s12042-013-9130-4

Rhizomes are underground stems that serve various purposes including vegetative propagation, invasion of new territory, and bioactive compound synthesis and storage. An important rhizomatous plant is sacred lotus (Nelumbo nucifera), which is prized in Asia as a medicine and a food. RNA-seq and total transcriptome analysis of rhizomes and other lotus tissues was applied to identify genes involved in rhizome growth, development and metabolism. Root, petiole, rhizome internode, and leaf tissues were used for single-read RNA-seq analysis. Two whole transcriptome paired-end read libraries from rhizome apical tip and elongation zone tissues were also generated in order to survey gene expression profiles. In this analysis, 22,803 genes were expressed: 20,476 in rhizome apical meristem and elongation zone, 17,171 in rhizome internode, 16,656 in leaf, 19,457 in root, and 16,845 in petiole. Gene ontology (GO) analysis indicated that “other membrane”, “nucleotide binding”, and “other cellular processes” were highly represented in the expressed genes. A total of 231 genes displayed rhizome-specific expression including several transcription factors, protein kinases, cytochromes P450 and a sulfate transporter. GOseq analysis showed that genes in the “molecular function” GO category and several genes related to cell proliferation based on KEGG IDs were preferentially up-regulated in rhizome tissue. In addition, 1,251 possible exon-skipping events were observed in 1,149 gene models. These results provide valuable insight into gene expression profiles and regulation in sacred lotus, and the identified rhizome-specific genes provide insight into important processes involved in the biology and development of sacred lotus rhizomes.