Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues

Colorectal cancer(CRC)is the third leading cancer globally.Metagenomics has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus-or species-level comparisons,providing evidence of dysbiosis in CRC development.However,this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in CRC.Here,we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal experiments.Through genomic comparison,these strains were divided into five phylogroups.The representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte(THP-1 cell)-based Transwell and animal experiments.Further bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms,genes,and metabolic pathways in the different phylogroups,which can improve the current understanding of the phenotypic differences between these strains.The strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria.

Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced(TAIL)-PCR

Whole-genome genotyping(WGG)stands as a pivotal element in genomic-assisted plant breeding.Nevertheless,sequencing-based approaches for WGG continue to be costly,primarily owing to the high expenses associated with library preparation and the laborious protocol.During prior development of foreground and background integrated genotyping by sequencing(FBI-seq),we discovered that any sequence-specific primer(SP)inherently possesses the capability to amplify a massive array of stable and reproducible non-specific PCR products across the genome.Here,we further improved FBI-seq by replacing the adapter ligated by Tn5 transposase with an arbitrary degenerate(AD)primer.The protocol for the enhanced FBI-seq unexpectedly mirrors a simplified thermal asymmetric interlaced(TAIL)-PCR,a technique that is widely used for isolation of flanking sequences.However,the improved TAIL-PCR maximizes the primer-template mismatched annealing capabilities of both SP and AD primers.In addition,leveraging of next-generation sequencing enhances the ability of this technique to assay tens of thousands of genome-wide loci for any species.This cost-effective,user-friendly,and powerful WGG tool,which we have named TAIL-PCR by sequencing(TAIL-peq),holds great potential for widespread application in breeding programs,thereby facilitating genome-assisted crop improvement.

The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation

Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing

Whole-genome genotyping methods are important for breeding.However,it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species.In our study,we accidently discovered that in adapter ligation-mediated PCR,the amplification by primertemplate mismatched annealing(PTMA)along the genome could generate thousands of stable PCR products.Based on this observation,we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing(FBI-seq)using one specific primer,in which foreground genotyping is performed by primer-template perfect annealing(PTPA),while background genotyping employs PTMA.Unlike DNA arrays,multiple PCR,or genome target enrichments,FBI-seq requires little preliminary work for primer design and synthesis,and it is easily adaptable to different foreground genes and species.FBI-seq therefore provides a prolific,robust,and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the postgenomics era.

The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize

Southern corn rust(SCR),caused by the fungal pathogen Puccinia polysora,is a major threat to maize pro-duction worldwide.Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR.Here,we report the molecular cloning and characterization of RppC,which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus.Further-more,we identified the corresponding avirulence effector,AvrRppC,which is secreted by P.polysora and triggers RppC-mediated resistance.Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance,indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production.Currently,RppC is the most frequently deployed SCR resistance gene in China,and a better understanding of its mode of action is crit-ical for extending its durability.

High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China over the past decade.Here,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried out.The PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye assemblers.The combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing process.The assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly index.Furthermore,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,respectively.Based on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a reference.The de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

Effort and Contribution of T-DNA Insertion Mutant Library for Rice Functional Genomics Research in China:Review and Perspective

With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.

利用培养组学技术分离鉴定体外降解胆固醇肠道细菌及其功能评价

高胆固醇是诱发心脑血管疾病的重要因素之一。目前国内外降低胆固醇的主要方式是药物治疗,但其存在费用高及副作用多的弊端。研究表明,肠道细菌对机体的胆固醇代谢有重要影响,但降胆固醇肠道细菌的筛选方式及功能评价却少有报道。本研究通过培养组学方法,使用牛胆汁酸或人工混合胆汁酸作为筛选条件,从健康人体肠道筛选出36种耐胆汁酸细菌。以鼠李糖乳杆菌GG株(Lactobacillus rhamnosus GG,LGG)作为阳性对照,设置0 g/L、0.3 g/L、3 g/L三种胆汁酸浓度组,对耐胆汁酸细菌进行体外降胆固醇能力评估,确定奇异变形菌、斯氏普罗威登斯菌、普通变形菌等10种细菌为降胆固醇优势菌。随后对其中6种降胆固醇优势菌——奇异变形菌、斯氏普罗威登斯菌、普通变形菌、潘氏变形菌、污蝇解克杆菌、雷氏普罗威登斯菌进行体外降甘油三酯能力评估以及人工胃液耐受能力评估。结果显示,上述6株细菌体外降甘油三酯能力均优于LGG。伴随人工胃液pH值的下降和作用时间的延长,6株细菌的生存率均下降。上述筛选实验及功能评价为进一步开发潜在的降胆固醇细菌制品提供研究基础。