Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

Abstract

Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera)

“…The percentage of Q30 in each sample was no less than 92.09% ( Table S2 ). 93.21–94.41% clean reads of each sample were mapped to the lotus genome ( Li et al, 2021 ). Hierarchical clustering was performed for the samples based on the correlation coefficient (R 2 ).…”

“…Currently, the lotus genome of ‘China Antique’ had been sequenced and released providing a research basis for omic study and breeding ( Ming et al, 2013 ; Li et al, 2021 ). DEGs involved in petaloid carpel were identified with transcriptomic analysis in P, Cp, and C. For the above candidate genes ( Fig.…”

“…Clean data was deposited in BMKCloud ( https://www.biocloud.net/ ) for analysis. We mapped the data to the reference genome of Nelumbo nucifera (ASM1431973v1) ( Li et al, 2021 ) using HiSat2 Software v2.0.4 ( Kim, Langmead & Salzberg, 2015 ). Transcript assembly, differential expression, and divergent regulation were performed using Cufflinks v2.1.1 ( Trapnell et al, 2010 ).…”

Comprehensive Analysis for GRF Transcription Factors in Sacred Lotus (Nelumbo nucifera)

“…N. nucifera , A. thaliana , O. sativa , and Ny. colorata genomics data were downloaded from the Nelumbo Genome Database ( , accessed on April 2022) [ 35 ] and the National Center for Biotechnology Information (NCBI, , accessed on 1 April 2022). The protein sequences of the GRF gene family of A. thaliana and O. sativa were downloaded from the TAIR database ( , accessed on 1 April 2022) and NCBI ( , accessed on 1 April 2022), respectively.…”

“…The gene expression matrix of different organs (young leaf, mature leaf, flower bud, rhizome internode, rhizome apical meristem, rhizome elongation zone, petal, immature receptacle, mature receptacle, unpollinated carpel, pollinated carpel, mature stamen, immature stamen, and seed coat and cotyledon on different development days) of ‘China Antique’ was downloaded from the Nelumbo Genome Database ( , accessed on 1 April 2022) [ 35 ]; the expression levels of NuGRFs were calculated as fragments per kilobase of exon per million fragments mapped (FPKM), the average of multiple samples was calculated, and TBtools was used to visualize the heatmap [ 36 ].…”