LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study

Abstract

Besides its important significance in plant taxonomy and phylogeny, sacred lotus (Nelumbo nucifera Gaertn.) might also hold the key to the secrets of aging, which attracts crescent attentions from researchers all over the world. The genetic or molecular studies on this species depend on its genome information. In 2013, two publications reported the sequencing of its full genome, based on which we constructed a database named as LOTUS-DB. It will provide comprehensive information on the annotation, gene function and expression for the sacred lotus. The information will facilitate users to efficiently query and browse genes, graphically visualize genome and download a variety of complex data information on genome DNA, coding sequence (CDS), transcripts or peptide sequences, promoters and markers. It will accelerate researches on gene cloning, functional identification of sacred lotus, and hence promote the studies on this species and plant genomics as well.Database URL: http://lotus-db.wbgcas.cn.

The NnCenH3 protein and centromeric DNA sequence profiles of Nelumbo nucifera Gaertn. (sacred lotus) reveal the DNA structures and dynamics of centromeres in basal eudicots

“…Although several studies have shown that centromeric heterochromatin is incompatible with gene expression (Schmid et al ., ; Lomiento et al ., ), the existence of active genes at the CenH3 subdomain in certain plant species has been proposed (Yan et al ., ; Gong et al ., ; Li et al ., ). Based on the lotus genome annotation database from LOTUS‐DB (Wang et al ., ), 210 annotated non‐transposable element (non‐TE) genes were discovered in NnCBSs (Figure S4; Table S1) in the present study. Of these genes, 92% (194 of 210) were located in the NnH3 (Histone H3 protein in sacred lotus) subdomains, and 7% (15 of 210) of the NnCBS‐associated genes were in the NnCenH3 subdomains; gene NNU_08544 (indicated by green and red arrows in Figure a, megascaffold 47) crossed both subdomain regions in megascaffold 47.…”

“…The annotated gene expression (FPKM) was obtained from the transcript file of the reference sacred lotus genome, LOTUS‐DB 1.0 (http://lotus-db.wbgcas.cn; Wang et al ., ). The transcription levels of 16 NnCenH3‐associated genes were verified by RT‐PCR.…”

“…ChIP‐ed DNA (10 ng) was submitted to the Beijing Genomics Institute (BGI, http://www.genomics.cn) for ChIP‐seq library construction and sequencing on the Illumina Hiseq 2000 platform. Over 20 million clean reads were aligned with the sacred lotus genome from LOTUS‐DB 1.0 (http://lotus-db.wbgcas.cn; Wang et al ., ) using the soap 2 aligner. To identify the NnCenH3 domains, ChIP‐seq read‐enriched regions were analyzed by sicer 1.1, using the parameters described by Gong et al .…”

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

“…Variant calling from lotus re-sequencing data To identify variants from lotus samples, the clean resequencing reads were mapped to the lotus reference genome 'China Antique' (http://lotus-db.wbgcas.cn/) by the BWA with 'mem' method and the parameters of '-t 10 -k 32-M' (Li and Durbin 2010;Wang et al 2015). The sam files from BWA were converted to bam format by samtools (Li et al 2009).…”

Evolution of floral diversity: genomics, genes andgamma

“…Source of datasets for the 30 species included in this study. 1KP, 1000 Green Plant Transcriptome Project [118]; AAGP, Ancestral Angiosperm Genome Project [119], Lotus-DB [120,121], Phytozome [122,123]. (5) 107 (40) 19 (4) 61 (30) 102 (55) 16 ( and paralogous gene lineages have assumed roles in floral symmetry, regulation of vegetative branching and unknown functions in flowers [131][132][133][134].…”