The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine

Hemerocallis citrina Borani(huang hua cai in Chinese)is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia.Here we assembled a high-quality reference genome of H.citrina using single-molecule sequencing and Hi-C technologies.The genome assembly was 3.77 Gb and consisted of 3183 contigs with a contig N50 of 2.09 Mb,which were further clustered into 11 pseudochromosomes.A larger portion(3.25 Gb or 86.20%)was annotated as a repetitive content and 54,295 protein-coding genes were annotated in the genome.Genome evolution analysis showed that H.citrina experienced a recent whole-genome duplication(WGD)event at~15.73 million years ago(Mya),which was the main factor leading to many multiple copies of orthologous genes.We used this reference genome to predict 20 genes involved in the rutin biosynthesis pathway.Moreover,our metabolomics data revealed neither colchicine nor its precursors in H.citrina,challenging the long-standing belief that this alkaloid causes poisoning by the plant.The results of our disruptive research are further substantiated by our genomic finding that H.citrina does not contain any genes involved in colchicine biosynthesis.The high-quality genome lays a solid foundation for genetic research and molecular breeding of H.citrina.

Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans

Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

An integrated strategy toward comprehensive characterization and quantification of multiple components from herbal medicine: An application study in Gelsemium elegans

Objective: To develop a powerful integrated strategy based on liquid chromatography coupled with mass spectrometry(LC-MS) systems for the comprehensive characterization and quantification of multiple components of herbal medicines.Methods: Firstly, different mobile phase additives, analysis time, and MS acquisition modes were orthogonally tested with liquid chromatography coupled with quadrupole time-of-flight mass spectrometry(LC-QTOF/MS) in order to detect as many components of Gelsemium elegans as possible with high peak intensity. Secondly, several data mining strategies, including database searching, diagnostic ion filtering and neutral loss filtering, were utilized to perform chemical profiling. Subsequently, this study focused on the quantification and validation of the performance of a liquid chromatography-triple mass spectrometry(LC-Qq Q/MS) assay based on derivative multiple reaction monitoring(De MRM).Results: A total of 147 components from G. elegans were characterized, among them 116 nontarget components were reported for the first time. A sensitive and reproducible LC-Qq Q/MS method was successfully developed and validated for the simultaneous relative quantification of 41 components of G. elegans.This LC-Qq Q/MS method was then applied to compare the contents of components in the roots, stems and leaves.Conclusion: The present integrated strategy would significantly contribute to chemical studies on herbal medicine, and its utility could be extended to other research fields, such as metabolomics, quality control,and pharmacokinetics.

Early weaning leads to the remodeling of lipid profile in piglet jejunal crypt cells during post-weaning days

Reportedly,proteins involved in lipid metabolism change significantly in the jejunal crypt cells of earlyweaned piglets,but the exact lipid profile change remains uncertain.In the present study,32 piglets weaned at 21 d of age were randomly divided into 4 groups with 8 replicates.The jejunal crypt cells of a group of piglets on the post-weaning day(PWD)1,3,7,and 14 were isolated per time point.Crypt cell lipid profiles were analyzed using ultra-high-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry.This study showed that piglets suffered the greatest weaning stress on PWD 3 in terms of the lowest relative weight of the small intestine,the highest relative weight of the spleen,and the highest levels of malondialdehyde,cholesterol,and low-density lipoprotein cholesterol.The lipid profile of jejunal crypt cells including carnitine,sulfatide,sphingomyelin,hexosylceramide,and ceramide greatly changed after weaning,especially between PWD3 and 14(P<0.05).The differential lipid species between these 2 d were mainly involved in the glycerophospholipid metabolism pathway.In addition,potential lipid biomarkers for weaning stress in crypt cells such as phosphatidylcholine(PC)(9:0/26:1),PC(17:0/18:2),carnitine(24:0),carnitine(22:0),sphingomyelin(d14:1/22:0),PC(P-18:0/18:4),phosphatidylethanolamine(P-16:0/20:4),phosphatidylinositol(15:1/24:4),and dihexosylceramide(d14:1/26:1)were identified.The changes in lipid profile might be related to the inflammation caused by early weaning.These findings might provide new therapeutical targets for intestinal dysfunctions caused by weaning stress.