Map-based cloning in crop plants: tomato as a model system II. Isolation and characterization of a set of overlapping yeast artificial chromosomes encompassing the jointless locus

Constructs carrying the entire or part of the tobacco nitrate reductase cDNA (NIA) cloned between the promoter and terminator sequences of the 35S RNA of the cauliflower mosaic virus were introduced into tobacco, in an attempt to improve nitrate assimilation. Several transgenic plants that had elevated NIA mRNA and nitrate reductase (NR) activity were obtained. In addition, a few plants that exhibited a chlorotic phenotype characteristic of NR-deficient mutants were also obtained. One of these plants contained no NIA mRNA, no NR activity and accumulated nitrate. This phenotype was therefore assumed to result from co-suppression of 35S-NIA transgenes and host NIA genes. NR-deficient plants were also found among the progeny of transformants overexpressing NIA mRNA. Genetic analyses indicated that these NR-deficient plants were homozygous for the 35S-NIA transgene, although not all homozygous plants were deficient for NR. The ratio of normal to NR-deficient plants in the progeny of homozygous plants remained constant at each generation, irrespective of the state of expression of the NIA genes (active or inactive) in the previous generation. This ratio also remained unchanged when field trials were performed in two areas of France: Versailles and Bergerac. The analysis of homozygous plants revealed that co-suppression was reversible at some stage of sexual reproduction. Indeed, host genes and transgenes reactivated at each generation, and co-suppression always appeared after a lag period of normal growth, suggesting that the phenomenon is developmentaly regulated. We observed that the triggering of cosuppression was delayed when plants were initially grown under limited light and/or watered with limited nitrate supply (light and nitrate both being required for the expression of the host NIA genes). However, this delay did not affect the final ratio between normal and NR-deficient plants after transfer to nitrate-fertilized fields. Independent transformants exhibited either different co-suppression ratios or no co-suppression at all, irrespective of the transgene copy number, suggesting that genomic sequences surrounding the transgene might play a role in determining co-suppression.     

An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning

The isolation of high quality megabase DNA from plant cells that is susceptible to a variety of molecular reagents is a critical first step in the physical analysis of complex genomes. A method for the isolation of such DNA by encapsulating plant protoplasts in agarose microbeads is presented. In comparison with the conventional agarose plug method, microbeads provide a dramatic increase in the surface area yielding megabase DNA that can be treated essentially as an aqueous DNA solution. Examples of the utility of DNA prepared by this technique for physical mapping, partial restriction enzyme digestion and cloning of large inserts as YACs are presented.     

Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population

Rice is a leading grain crop and the staple food for over half of the world population. Rice is also an ideal species for genetic and biological studies of cereal crops and other monocotyledonous plants because of its small genome and well developed genetic system. To facilitate rice genome analysis leading to physical mapping, the identification of molecular markers closely linked to economic traits, and map-based cloning, we have constructed two rice bacterial artificial chromosome (BAC) libraries from the parents of a permanent mapping population (Lemont and Teqing) consisting of 400 F9 recombinant inbred lines (RILs). Lemont (japonica) and Teqing (indica) represent the two major genomes of cultivated rice, both are leading commercial varieties and widely used germplasm in rice breeding programs. The Lemont library contains 7296 clones with an average insert size of 150 kb, which represents 2.6 rice haploid genome equivalents. The Teqing library contains 14208 clones with an average insert size of 130 kb, which represents 4.4. rice haploid genome equivalents. Three single-copy DNA probes were used to screen the libraries and at least two overlapping BAC clones were isolated with each probe from each library, ranging from 45 to 260 kb in insert size. Hybridization of BAC clones with chloroplast DNA probes and fluorescent in situ hybridization using BAC DNA as probes demonstrated that both libraries contain very few clones of chloroplast DNA origin and are likely free of chimeric clones. These data indicate that both BAC libraries should be suitable for map-based cloning of rice genes and physical mapping of the rice genome.     

橡胶草90年来主要研究成果及最新研究进展

天然橡胶是重要的国防战略物质,巴西橡胶树（Hevea brasiliensis（Willd.ex A.Juss.） Muell.Arg）是天然橡胶的唯一来源,天然橡胶商业化形式极为单一,潜在的供给不足问题亟待解决。因此,寻找可替代巴西橡胶树的产胶植物一直受到全世界高度重视。蒲公英属橡胶草（Taraxacum kok-saghyz Rodin）根部含有与橡胶树橡胶类似的天然橡胶分子,该植物主要分布在温带和寒带地区,具有易于机械化收获、生长周期短、遗传转化相对容易等特点,是最具开发潜力的产胶植物。本文对橡胶草90年（1931-2018）来的研究历史和主要成果进行了概括,对近10年取得的最新成果进行了深度分析,并预测橡胶草在未来天然橡胶产业中的作用,期望为开展橡胶草商业化生产和橡胶生物合成相关基础研究提供一定的参考。     

CRISPR/Cas9介导靶向敲除拟南芥BRI1突变体的鉴定

以拟南芥(Arabidopsis thaliana)油菜素内酯受体BRI1为目的基因,利用CRISPR/Cas9基因编辑技术定向编辑拟南芥BRI1,以期获得更多BRI1的突变体,为后续BRI1功能的进一步深入研究奠定基础。通过筛选转基因植株,对编辑后的BRI1进行测序分析,结果显示该突变体中BRI1基因序列由于新碱基的插入导致提前终止。同BRI1强突变体bri1-710一样,相比于野生型对照均对BL处理不敏感,但相比于bri1-710,该突变体植株较大,暗示BRI1 N端可能在BR信号途径中有重要作用。因此该研究可为后续进一步研究拟南芥及其他同源物种的BRI1功能提供可靠的参考依据。     

Panamonon A and B,a pair of novel tetrahydrobenzofuran derivatives from Litsea panamonja (Nees) Hook. f.

A pair of novel tetrahydrobenzofuran derivatives with a unique C₁₈ carbon skeleton, panamonon A (1) and B (2), was isolated from the leaves and twigs of Litsea panamonja (Nees) Hook. f. These new compounds contain an unprecedented C₁₈ carbon skeleton consisting of a characteristic tetrahydrobenzofuran-2,5(3H,6H)-dione core with a biosynthetically extended geranyl side chain, designated as “panamonane”.

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Highlights? A pair of novel tetrahydrobenzofuran derivatives with a unique C₁₈ carbon skeleton was isolated. ? The new compounds possess an unprecedented C₁₈ carbon skeleton and are designated as “panamonane”. ? They are featured with a tetrahydrobenzofuran-2,5(3H,6H)-dione moiety and a geranyl side chain. ? The plausible biosynthetic pathways of them were discussed.     

The Mitochondrial Genome of Paramphistomum cervi (Digenea), the First Representative for the Family Paramphistomidae

We determined the complete mitochondrial DNA (mtDNA) sequence of a fluke, Paramphistomum cervi (Digenea: Paramphistomidae). This genome (14,014 bp) is slightly larger than that of Clonorchis sinensis (13,875 bp), but smaller than those of other digenean species. The mt genome of P. cervi contains 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (NCRs), a complement consistent with those of other digeneans. The arrangement of protein-coding and ribosomal RNA genes in the P. cervi mitochondrial genome is identical to that of other digeneans except for a group of Schistosoma species that exhibit a derived arrangement. The positions of some transfer RNA genes differ. Bayesian phylogenetic analyses, based on concatenated nucleotide sequences and amino-acid sequences of the 12 protein-coding genes, placed P. cervi within the Order Plagiorchiida, but relationships depicted within that order were not quite as expected from previous studies. The complete mtDNA sequence of P. cervi provides important genetic markers for diagnostics, ecological and evolutionary studies of digeneans.     

志贺菌基因组进化研究进展

志贺菌属(Shigella)是引起全球范围内细菌性痢疾的重要病原菌.近年来,多重耐药型和新血清型志贺菌的不断出现给志贺菌的监测和防控带来了新的挑战.基因组学的快速发展为深入了解志贺菌的进化来源、变异机制及传播规律等提供了极大的帮助,对控制细菌性痢疾的蔓延具有重要的科学意义.本文首先从遗传来源角度探讨志贺菌与大肠杆菌的进化关系及其可能的分子机制,随后对福氏、宋内和1型痢疾志贺菌的基因组进化进展进行了总结,详细描述了它们的时空分布特点以及耐药基因变异在进化中所发挥的作用,以期为志贺菌的研究和防控提供参考.     

Down-regulated expression of LINC00518 prevents epithelial cell growth and metastasis in breast cancer through the inhibition of CDX2 methylation and the Wnt signaling pathway

Breast cancer (BC)-related mortality is associated with the potential metastatic properties of the primary breast tumors. The following study was conducted with the main focus on the effect of LINC00518 on the growth and metastasis of BC epithelial cells via the Wnt signaling pathway through regulation of the methylation of CDX2 gene. Initially, differentially expressed long intergenic non-protein coding RNAs (lincRNAs) related to BC were screened out in the Cancer Genome Atlas (TCGA) database, after which we detected the LINC00518 expression and localization in BC tissues and cells. Then the CDX2 positive expression and methylation level were identified. The targeting relationship of LINC00518 and CDX2, and binding methyltransferase in the promoter region were examined. BC epithelial cell proliferation, colony formation ability, invasion, migration and apoptosis were further evaluated. The lincRNA expression data related to BC downloaded from the TCGA database revealed that there was a high expression of LINC00518 in BC, and a negative correlation between LINC00518 and CDX2. In addition, LINC00518 promotes CDX2 methylation by recruiting DNA methyltransferase through activating the Wnt signaling pathway. The down-regulation of LINC00518 inhibited proliferation, invasion, migration, and EMT of BC epithelial cells while enhancing apoptosis. The inhibitory effects of LINC00518 down-regulation was reversed by CDX2 down-regulation. In conclusion, our findings revealed that down-regulation of LINC00518 might have the ability to suppress BC progression by up-regulating CDX2 expression through the reduction of methylation and blockade of the Wnt signaling pathway, resulting in the inhibition of proliferation and promotion of apoptosis of BC epithelial cells.