Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.)

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).     

Genome-Wide Identification and Characterization of Nucleotide-Binding Site (NBS) Resistance Genes in Pineapple

Pineapple is a major tropical fruit and the most important crop processing CAM photosynthesis. It originated in southwest Brazil and northeast Paraguay and survived the harsh, semi-arid environment. Disease resistance genes have contributed to the survival and thriving of this species. The largest class of disease resistance (R) genes in plants consists of genes encoding nucleotide-binding site (NBS) domains. The sequenced genome of pineapple (Ananas comosus (L.) Merr.) provides a resource for analyzing the NBS-encoding genes in this species. A total of 177 NBS-encoding genes were identified using automated and manual analysis criteria, and these represent about 0.6 % of the total number of predicted pineapple genes. Five genes identified here contained the N-terminal Toll/Interleukin-l receptor (TIR) domain, and 46 genes carried the N-terminal Coiled-Coil (CC) motif. A majority of these NBS-encoding genes (84 %) contained a leucine-rich repeat (LRR) domain. A total of 130 of 177 (73 %) of these NBS-encoding genes were distributed across 20 pineapple linkage groups. The identification and characterization of NBS genes in pineapple yielded a valuable genomic resource and improved understanding of R genes in pineapple, which will facilitate the development of disease resistant pineapple cultivars.     

Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera)

Genomic resources such as single nucleotide polymorphism (SNPs), insertions and deletions (InDels) and SSRs (simple sequence repeats) are essential for crop improvement and better utilization in genetic breeding. However, the resources for the sacred lotus (Nelumbo nucifera Gaertn.) are still limited. In the present study, to dissect large-scale genomic molecular marker resources for sacred lotus, we re-sequenced a Thailand sacred lotus cultivar ‘Chiang Mai wild lotus’ and compared with the reported lotus genome ‘Middle lake wild lotus’. A total of 3,180,059 SNPs, 328, 251 InDels and 14,191 SVs were found between the two genomes. The functional impact analyses of these SNPs indicated that they may be involved in metabolic processes, binding, catalytic activity, etc. Mining the genome sequences for SSRs showed that 191,657 SSRs were identified with a frequency of one SSR per 4.23 kb and 103,656 SSR primer pairs were designed. Furthermore, 14, 502 EST-SSRs were also indentified using the available RNA-seq data in the NCBI. A subset of 150 SSRs (genomic and EST-SSRs) was randomly selected for validation and genetic diversity analysis. The genotypes could be easily distinguished using these SSR markers and the ‘Chiang Mai wild lotus’ was obviously differentiated from the other Chinese accessions. This study provides considerable amounts of genomic resources and markers for the quantitative trait locus (QTL) identification and molecular selection of the species, which could have a potential role in various applications in sacred lotus breeding.     

Changes of Thylakoid Membrane Stacks and Chl a/b Ratio of Chloroplast from Sacred Lotus (Nelumbo nucifera) Seeds During Their Germination Under Light

Changes of chloroplast thylakoid membrane stacks and Chl a/b ratio in the plumule of sacred lotus (Nelumbo nucifera Gaertn) seeds during their germination under light were as follows: Before germination there were giant grana and very low Chi a/b ratio (0.9) in the chloroplasts. Two days after germination, the thylakoid membranes of the giant grana gradually loosened and even destacked (disintegrated), the Chl a/b ratio was 1.06. Four clays after germination, the newly formed grana thylakoid membranes were 3–5 times shorter than those of the supergrana thylakoid membranes before germination and less grana stacks were seen; the Chl a/b ratio was 1.42. Six days after germination, the stacked thylakoi membranes became more orderly arranged. In addition the grana increased in number, the stroma thylakoid membranes were scarce, the Chl a/b ratio was 2.16. Eiglt days after germination, the thylakoid membranes in each granum decreased, but the total number of grana increased only slightly. In the meantime, some large starch grains and more stroma thylakoid membranes appeared; the Chl a/b ratio was 2.77. Ten days after germination normal thylakoid membrane structure was formed both in grana and stroma lamellae. They were arranged orderly as in the chloroplasts of other higher plants; the Chl a/b ratio was 2.80. The following conclusions could be drawn from the above mentioned results: 1) There was a negative correlation between the degree of stacking of the grana thylakoid membranes and the Chl a/b ratio. This statement further proved that the membranes stacking might mainly be induced by LHCII. 2) Development of the grana thylakoid membranes within chloroplasts from sacred lotus plumule followed that of the stroma thylakoid membranes, and the tendency of changes of their Chl 2/b ratio being from the lowest to the highest and then to normal were quite different from those of other higher plants. The chloroplasts iri the latter plants contain long parallel stacks of nonappressed primary thylakoids at second step, and the changes of their ratio of Chl a/b tend to be from the highest to the lowest and then to normal. There are indications that sacred lotus plumule might employ a distinctive developing pathway. This provides an important basis for Nelumbo to possess an unique position in phylogeny of Angiospermae.