Integrated Lipidomic and Transcriptomic Analysis Reveals Lipid Metabolism in Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica) as the main traditional crop in China, is rich in many kinds of high quality fatty acids (FAs). In this study, Ultra-high performance liquid chromatography-time-of-flight-tandem mass spectrometer (UHPLC-Q-TOF-MS/MS) was used to determine the lipids of JG35 and JG39. A total of 2,633 lipid molecules and 31 lipid subclasses were identified, mainly including thirteen kinds of glycerophospholipids (GP), eleven kinds of glycerolipids (GL), four kinds of sphingolipids (SP), two kinds of fatty acyls (FA) and one kind of sterol (ST). Among them JG35 had higher contents of diacylglycerols (DG) and ceramides (Cer), while triacylglycerols, phosphatidyl ethanolamine, phosphatidic acid, sterol, fatty acyls and pardiolipin (TG, PE, PA, ST, FA and CL) were higher in JG39. Meantime, the correlation analysis of lipidomics and transcriptomics was used to map the main differential lipid metabolism pathways of foxtail millet. The results shown that a differentially expressed genes (DEGs) of FATA/B for the synthesis of FA was highly expressed in JG35, and the related genes for the synthesis DG (ACCase, KAS, HAD, KCS, LACS and GAPT), TG (DGAT and PDAT) and CL (CLS) were highly expressed in JG39. The results of this study will provide a theoretical basis for the future study of lipidomics, improvement of lipid quality directionally and breeding of idiosyncratic quality varieties in foxtail millet.

Download Full-text

De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

10.21203/rs.3.rs-143813/v1 ◽

2021 ◽

Author(s):

Jie Wang ◽

Shiming Li ◽

Lei Lan ◽

Mushan Xie ◽

Shu Cheng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Sequence ◽

Reference Genome ◽

Foxtail Millet ◽

Setaria Italica ◽

Genome Comparison ◽

Sequencing Technology ◽

High Quality ◽

Next Generation Sequencing Technology ◽

Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

Download Full-text

A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.)

Scientific Reports ◽

10.1038/s41598-019-52786-2 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Dan Liu ◽

Yanjiao Cui ◽

Suying Li ◽

Guihua Bai ◽

Qiang Li ◽

...

Keyword(s):

Nuclear Dna ◽

Foxtail Millet ◽

Leaf Tissue ◽

Setaria Italica ◽

Future Research ◽

High Quality ◽

Chloroplast Genomes ◽

Zea May ◽

Chloroplast Genome Sequence ◽

Sequence Quality

Abstract The complexity of the leaf constitution of foxtail millet (Setaria italica (L.) P. Beauv.) makes it difficult to obtain high-purity cpDNA. Here, we developed a protocol to isolate high-quality cpDNA from foxtail millet and other crops. The new protocol replaces previous tissue grinding and homogenization by enzyme digestion of tiny leaf strips to separate protoplasts from leaf tissue and protects chloroplasts from damage by undue grinding and homogenization and from contamination of cell debris and nuclear DNA. Using the new protocol, we successfully isolated high-quality cpDNAs for whole-genome sequencing from four foxtail millet cultivars, and comparative analysis revealed that they were approximately 27‰ longer than their reference genome. In addition, six cpDNAs of four other species with narrow and thin leaf blades, including wheat (Triticum aestivum L.), maize (Zea may L.), rice (Oryza sativa L.) and sorghum (Sorghum bicolor (L.) Moench), were also isolated by our new protocol, and they all exhibited high sequence identities to their corresponding reference genomes. A maximum-likelihood tree based on the chloroplast genomes we sequenced here was constructed, and the result was in agreement with previous reports, confirming that these cpDNA sequences were available for well-supported phylogenetic analysis and could provide valuable resources for future research.

Download Full-text

Transforming of Triptolide into Characteristic Metabolites by the Gut Microbiota

Molecules ◽

10.3390/molecules25030606 ◽

2020 ◽

Vol 25 (3) ◽

pp. 606

Author(s):

Ran Peng ◽

Shu-Rong Ma ◽

Jie Fu ◽

Pei Han ◽

Li-Bin Pan ◽

...

Keyword(s):

Mass Spectrometry ◽

Gut Microbiota ◽

Theoretical Basis ◽

High Performance ◽

Ion Trap ◽

Liver Microsomes ◽

Tandem Mass ◽

Molecular Weights ◽

Intestinal Contents ◽

First Time

The importance of the gut microbiota in drug metabolism, especially in that of nonabsorbable drugs, has become known. The aim of this study was to explore the metabolites of triptolide by the gut microbiota. With high-performance liquid chromatography coupled with tandem mass spectrometry and ion trap time-of-flight multistage mass spectrometry (LC-MS/MS and LC/MSn-IT-TOF), four metabolites of triptolide (M1, M2, M3, and M4) were found in the intestinal contents of rats. M1 and M2, were isomeric monocarbonyl-hydroxyl-substituted metabolites with molecular weights of 390. M3 and M4 were isomeric dehydrogenated metabolites with molecular weights of 356. Among the four metabolites, the dehydrogenated metabolites (M3 and M4) were reported in the gut microbiota for the first time. The metabolic behaviors of triptolide in the gut microbiota and liver microsomes of rats were further compared. The monocarbonyl-hydroxyl-substituted metabolites (M1 and M2) were generated in both systems, and another monohydroxylated metabolite (M5) was found only in the liver microsomes. The combined results suggested that the metabolism of triptolide in the gut microbiota was specific, with two characteristic, dehydrogenated metabolites. This investigation might provide a theoretical basis for the elucidation of the metabolism mechanism of triptolide and guide its proper application in clinical administration.

Download Full-text

A Method for Measuring the Lipophilicity of Compounds in Mixtures of 10

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057110396372 ◽

2011 ◽

Vol 16 (3) ◽

pp. 348-355 ◽

Cited By ~ 26

Author(s):

Mark C. Wenlock ◽

Tim Potter ◽

Patrick Barton ◽

Rupert P. Austin

Keyword(s):

High Performance ◽

Shake Flask ◽

Distribution Coefficients ◽

Ion Pair ◽

Drug Candidate ◽

Tandem Mass ◽

Discovery Process ◽

Drug Discovery Process ◽

High Quality ◽

In Silico Models

Lipophilicity is an important parameter for any potential drug candidate. Accurate and efficient lipophilicity measurements facilitate the development of high-quality predictive in silico models that support the design of future drugs. Lipophilicity estimates derived from the traditional 1-octanol/water shake flask techniques have been the most widely employed and are therefore the best understood. This technique can be considered to give a good measure of a compound’s lipophilicity, albeit slower and more labor intensive to run compared with some other methodologies. Herein is described and validated an efficient 1-octanol/water shake flask technique that has sufficient capacity to be run as a primary screen within the drug discovery process. This is achieved by the simultaneous measurement of the distribution coefficients of mixtures of up to 10 compounds using high-performance liquid chromatography and tandem mass spectrometry. Concerns regarding ion pair partitioning that could result in erroneous results due to interactions between compounds within a mixture are discussed.

Download Full-text

De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

BMC Plant Biology ◽

10.1186/s12870-021-03003-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jie Wang ◽

Shiming Li ◽

Lei Lan ◽

Mushan Xie ◽

Shu Cheng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Sequence ◽

Reference Genome ◽

Foxtail Millet ◽

Setaria Italica ◽

Genome Comparison ◽

Sequencing Technology ◽

High Quality ◽

Next Generation Sequencing Technology ◽

Generation Sequencing

Abstract Background Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

Download Full-text