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whole-genome sequencing in medicinal plants:current progress and prospect

Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang Leng Wei Sun Baocai Liu Xue Feng Xiwen Li Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Agricultural Bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant genome”to decipher their genetic code.However,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity.whole genomes of 123 medicinal plants were published until September 2022.These published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing strategies.More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes.Diploid species account for a majority of sequenced medicinal plants.The whole genomes of plants in the Poaceae family are the most studied.Almost 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal effects.Medicinal plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to complete.In addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome.Herein,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants.Moreover,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were reviewed.We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

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Characterization of a novel Bacillus methylotrophicus phage BM-P1

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Food Quality and Safety 2023年第2期7卷 267-276页

作者： Ruirui Lv Ming Xu She Guo Jingwei Yao Hafiz Arbab Sakandar Jing Guo Can Zhang Xia Chen Inner Mongolia Agricultural University Key Laboratory of Dairy Biotechnology and EngineeringMinistry of EducationKey Laboratory o Dairy Products ProcessingMinistry of Agriculture and Rural AffairsInner Mongolia Key Laboratory of Dairy Biotechnology and Engineering Hohhot 010018China

Bacillus species have been widely used as probiotics in a number of food products.However,these are vulnerable to bacteriophage infections,which poses fermentation failure and eventually result in economic losses.Given this,we designed this study in which the bacteriophage of lysogenic Bacillus methylotrophicus,phage BM-P1,was induced successfully,and its biological characteristics and genome information were researched.The obtained results showed that phage BM-P1 belonged to Myoviridae family.The maximum number of infections for this phage was 10,with a burst size of 104.48±2.70 counts expressed per milliter per infective center.Additionally,this phage was temperature-and pH-sensitive and divalent ions(Ca2+,Mg2+)and chloramphenicol did not have a significant influence on its adsorption capacity.Genomic analysis revealed that the genome size of phage BM-P1 was 153087 bp with 41.94%GC content,including 258 coding sequences.Furthermore,52 bac-teriophages of Bacillus were classified into two clades by using phylogenetic analysis.Among them,phage BM-P1 with phage VB_BsuM-Goe3 and vB_BveM-Goe7 had the highest average nucleotide identity values,95.23%and 95.28%,respectively.However,synteny analysis revealed transposition,deletion,and insertion in the genome of BM-P1.Considering this,it could be extrapolated that this phage is a new lysogenic phage.In conclusion,this study furthers the knowledge on the properties of B.methylotrophicus phages and provides seminal insights for designingeffective antiphage strategiesforfermentation industry.

关键词： Bacillus methylotrophicus phage morphology resistance adsorption whole genome

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genome-wide analysis reveals signatures of complex introgressive gene flow in macaques(genus Macaca)

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Zoological Research 2021年第4期42卷 433-449页

作者： Yang Song Cong Jiang Kun-Hua Li Jing Li Hong Qiu Megan Price Zhen-Xin Fan Jing Li Key Laboratory of Bio-resources and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuan 610064China Institute of Animal Genetics and Breeding College of Animal Science and TechnologySichuan Agricultural UniversityChengduSichuan 611130China Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life SciencesSichuan UniversityChengduSichuan 610064China

The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification(about five million years ago)and rapid radiation of constituent species.To understand evolutionary gene flow in macaques,we sequenced four whole genomes(two M.arctoides and two M.thibetana)and combined them with publicly available macaque genome data for genome-wide analyses.We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals,with the strongest signals between the fascicularis and silenus species groups.Notably,we detected bidirectional gene flow between M.fascicularis and M.nemestrina.The estimated proportion of the genome inherited via gene flow between the two species was 6.19%.However,the introgression signals found among studied island species,such as Sulawesi macaques and M.fuscata,and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression.Furthermore,gene flow signals varied in individuals of the same species(M.arctoides,M.fascicularis,M.mulatta,M.nemestrina and M.thibetana),suggesting very recent gene flow after the populations split.Pairwise sequentially Markovian coalescence(PSMC)analysis showed all macaques experienced a bottleneck five million years ago,after which different species exhibited different fluctuations in demographic history trajectories,implying they have experienced complicated environmental variation and climate change.These results should help improve our understanding of the complicated evolutionary history of macaques,particularly introgressive gene flow.

关键词： Macaca whole genome Introgression Gene flow Demographic history

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Effect of Tiantai No.1(天泰1号)on Gene Expression Profiles in Hippocampus of Alzheimer's Disease Rats by Bioinformatic Analysis

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Chinese Journal of Integrative Medicine 2015年第2期21卷 123-131页

作者：李映红吴正治曹美群李明孙珂焕杨敏陈嫚茵黄长江 The First Affiliated Hospital of Shenzhen University The Second Clinical Medical College of Jinan University Larry Hillblom Islet Research Center David Geffen School of MedicineUCLA

Objective： To study the effect of Tiantai No. 1 （天泰1号） on gene expression profile in hippocampus of Alzheimer＇s disease （AD） rat, molecular genetic target points of the effect of this drug were defined, its molecular genetic pharmacodynamic mechanism of anti-AD was further explored at molecular gene level, and a scientific basis was provided for its clinical availability and promotion. Methods： Thirty male Sprague- Dawley rats were divided into three groups with 10 rats per group： sham-operation group, model group and Tiantai No. 1 group. Sterile surgical procedure was applied, the model group with bilateral hippocampal injection of Aβ21-40 was established, and normal saline was used instead of Aβ1-40 in the sham-operation group. One week after the models was made, rats were administered by gastric lavage once every day for three consecutive weeks. The rats of the sham-operation group and the model group were daily fed with purified water by lavage; the rats of the Tiantai No.1 group treated group were administered with Tiantai No.1 by lavage. Total RNAs of hippocampus tissues were extracted with Trizol, the changes of hippocampus gene expression profiles in the above throe groups were analyzed by using Affymetrix rat whole genome expression profile microarray. Results： Microarray analysis showed that, compared with the sham-operation group, the hippocampus of the model group had 50 up-regulated genes with significant difference （fold change 〉2）, and 21 down-rogulated genes with significant difference （fold change 〈0.5）; compared with the hippocampus of the model group, the hippocampus of the Tiantai No. 1 group was found to have 5 up-regulated genes with significant difference （fold change 〉2） and 20 down-regulated genes with significant difference （fold change 〈0.5）. The functions of differonUally expressed genes of the groups were involved in nervous system＇s development, neuronic differentiation and function-regulation, cellular growth and differentiation and apoptosis, synaptic occurrence and plasticity, inf

关键词： whole genome genome microarray gene expression profile Tiantai No. 1 Alzheimer＇s disease,hippocampus

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genome wide exploration of the origin and evolution of amino acids

Genome wide exploration of the origin and evolution of amino...

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中国空间科学学会第七次学术年会

作者： Xiao-Xia Liu Zhi-Liang Ji Yu-Feng Zhao (Xiamen University Xiamen 361005)

＜正＞Even after years of exploration,the terrestrial origin of bio-molecules remains unsolved and controversial.Today observation of amino acid composition in proteins has become an alternative way for global underst... 详细信息

关键词： Origin of amino acids whole genome Bioinformatics

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