TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis)

Extensive ICP-MS and HPLC-QQQ detections reveal the content characteristics of main metallic elements and polyphenols in the representative commercial tea on the market

The content of polyphenols and metal elements in tea has an important impact on the choice of consumers. In this study, we conducted a comparative analysis of ten elements including Fe, Mg, Al, Zn, Cu, Mn, Ni, Cr, Pb, and As in 122 representative tea samples from 20 provinces. The results showed that the difference of metal content among six tea categories was greater than that among provinces, and the overall metal content of black tea was relatively higher. The contents of all elements from high to low were: Mg > Mn > Al > Fe > Zn > Cu > Ni > Cr > Pb > As. The contents of Ni, Fe, Al, Zn and Mn showed significant differences among multiple types of tea categories. While the detection rates of Pb and As were 10.7 and 24.6%, respectively. The contents of all elements were in line with the national limit standards. Meanwhile, the relative contents of theanine, caffeine and a total of 53 polyphenolic compounds in 122 tea samples were detected. The analysis showed that the content of these compounds differed least between green and yellow tea, and the largest difference between black tea and oolong tea. This study provides important support for consumers to choose tea rationally.

PPGV: a comprehensive database of peach population genome variation

Peach tree is one of the most important fruit trees in the world, and it has been cultivated for more than 7,500 years. In recent years, the genome and population resequencing of peach trees have been published continuously, which has effectively promoted the research of peach tree genetics and breeding. In order to promote the further mining and utilization of these data, we integrated and constructed a comprehensive peach genome and variation database (PPGV, http://peachtree.work/home ). The PPGV contains 10 sets of published peach tree genome data, as well as genomic variation information for 1,378 peach tree samples (the resequencing data of 1,378 samples were aligned with the high-quality genomes of Lovell, CN14 and Chinesecling, respectively, for mutation detection). A variety of useful and flexible tools, such as BLAST, Gene ID Convert, KEGG/GO Enrichment, Primer Design and Gene function, were also specially designed for searching data and assisting in breeding.

GelFAP v2.0: an improved platform for Gene functional analysis in Gastrodia elata

BACKGROUND

Gastrodia elata (tianma), a well-known medicinal orchid, is widely used to treat various kinds of diseases with its dried tuber. In recent years, new chromosome-level genomes of G.elata have been released in succession, which offer an enormous resource pool for understanding gene function. Previously we have constructed GelFAP for gene functional analysis of G.elata. As genomes are updated and transcriptome data is accumulated, collection data in GelFAP cannot meet the need of researchers.

RESULTS

Based on new chromosome-level genome and transcriptome data, we constructed co-expression network of G. elata, and then we annotated genes by aligning with sequences from NR, TAIR, Uniprot and Swissprot database. GO (Gene Ontology) and KEGG (Kyoto Encylopaedia of Genes and Genomes) annotations were predicted by InterProScan and GhostKOALA software. Gene families were further predicted by iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid. Finally, we developed an improved platform for gene functional analysis in G. elata (GelFAP v2.0) by integrating new genome, transcriptome data and processed functional annotation. Several tools were also introduced to platform including BLAST (Basic Local Alignment Search Tool), GSEA (Gene Set Enrichment Analysis), Heatmap, JBrowse, Motif analysis and Sequence extraction. Based on this platform, we found that the flavonoid biosynthesis might be regulated by transcription factors (TFs) such as MYB, HB and NAC. We also took C4H and GAFP4 as examples to show the usage of our platform.

CONCLUSION

An improved platform for gene functional analysis in G. elata (GelFAP v2.0, www.gzybioinformatics.cn/Gelv2 ) was constructed, which provides better genome data, more transcriptome resources and more analysis tools. The updated platform might be preferably benefit researchers to carry out gene functional research for their project.