An aberrant plastid ribosomal RNA gene cluster in the root parasite Conopholis americana

The plastid ribisomal RNA (rRNA) operon of the achlorophyllous root parasite Conopholis americana was completely sequenced. Full-length rRNA genes are retained in the gene cluster, but significant divergence has occurred in the 16S, 23S and 5S genes. Both the 16S–23S intergenic spacer and the 4.5S–5S intergenic spacer have suffered substantial deletions, including the two tRNA genes typically found in prokaryotic and plastid 16S–23S spacers.     

Nucleotide sequence and phylogenetic implication of the ATPase subunits β and ε encoded in the chloroplast genome of the brown alga Dictyota dichotoma

We have cloned and sequenced the genes atpB and atpE, coding for CF₁ subunits and , respectively, of the chloroplast genome of the brown alga Dictyota dichotoma. Although the coding site of atpE cannot be demonstrated by heterologous Southern hybridizations, a 417 bp reading frame 3 to atpB was identified as the gene atpE by sequence similarities with atpE genes from other sources. A maximum sequence identity of 30% is found between the predicted amino acid sequence of the Dictyota subunit and the corresponding cyanobacterial subunits. Including conserved amino acid replacements, the Dictyota subunit exhibits about 70% sequence similarity with the cyanobacterial and land plant subunits. As in cyanobacteria, the atpE gene does not overlap the preceding gene atpB. The deduced amino acid sequence of atpB is 74–79% identical to the corresponding cyanobacterial and chloroplast subunits. Entirely conserved are regions referred to as the catalytic and/or regulatory sites of ATP formation, including interacting regions between subunits and . A phylogram predicted from F₁/CF₁- subunits of eleven different organisms suggests a common evolutionary origin of plastids from chlorophytes and brown algae.     

Construction and characterisation of a yeast artificial chromosome library containing three haploid maize genome equivalents

We have constructed a yeast artificial chromosome (YAC) library using high-molecular-weight DNA prepared from agarose-embedded leaf protoplasts of the maize inbred line UE95. This library contains 79 000 clones with an average insert size of 145 kb and should therefore represent approximately three haploid genome equivalents. The library is organised as an ordered array in duplicate microtitre plates. Forty-one pools of DNA from 1920 individual clones have been prepared for rapid screening of the library by the polymerase chain reaction (PCR). Using this approach, together with conventional colony hybridisation, we have been able to identify between one and eight positive clones for every probe used.     

一株鳢源鰤诺卡氏菌致病性与全基因组分析

【背景】鰤诺卡氏菌是一种典型的条件致病菌,感染鳢、鲈等多种名优鱼类,易造成存在机体损伤或免疫机能下降的鱼持续性感染,给水产养殖业造成了巨大损失。【目的】了解临床分离鳢源鰤诺卡氏菌对乌斑杂交鳢（斑鳢♀×乌鳢♂）的致病性,并从全基因组层面了解该病原菌的基因组和致病因子信息,为鰤诺卡氏菌后续病原学及鰤诺卡氏菌病防治技术和疫苗的开发研究提供有利的数据支撑。【方法】鰤诺卡氏菌NK201610020通过回归感染试验和发病鱼靶器官组织病理分析,了解鰤诺卡氏菌的毒力和病理特征。通过对试验菌进行全基因组测序和比较基因组学分析,挖掘该菌的基因组与毒力特征。【结果】回归感染试验结果显示,除1.5×10³组外,其余5个感染组致死率高达90%,LD₅₀为1.079×10³ CFU/mL,说明试验菌毒力较强。组织病理学观察到肝、脾、肾呈现严重的病理损伤,而且有肉芽肿结构形成。试验菌全基因组测序发现,全基因组大小为8294329bp,GC含量为68.10%,共预测到编码基因7812个。比较基因组学分析发现,不同地区不同宿主来源鰤诺卡氏菌在基因组基础特...     

尖孢镰孢菌果胶裂解酶基因家族鉴定及侵染表达模式分析

【背景】番茄枯萎病是番茄生产中常见的土传真菌病害。【目的】为鉴定番茄枯萎病基因组果胶裂解酶基因家族,明确该基因家族在侵染过程表达模式。【方法】采用生物信息学方法鉴定了番茄枯萎病尖孢镰孢菌(Fusarium oxysporum f. sp. Lycopersici)基因组内PEL基因家族,并分析了基因结构、染色体定位及三级结构,同时利用荧光定量PCR分析了FoPEL1-16基因在接种番茄根系的表达情况。【结果】番茄尖孢镰孢菌基因组内PEL基因家族成员有16个。氨基酸序列长度在163-548个氨基酸,信号肽长度在16-21个氨基酸。染色体定位分析表明16个基因在染色体上分布不均,分别定位在7条染色体上。根据基因结构和保守基序分析结果 16个基因可分为4类。进化分析表明该基因家族成员可聚成4支。三级结构预测结果显示同一家族存在相似结构域。荧光定量PCR分析结果表明Fo PEL基因在侵染过程表达水平明显上升。【结论】番茄尖孢镰孢菌基因组内果胶裂解酶以基因家族形式存在,其基因结构存在差异暗示了其功能多样性;FoPEL基因在侵染过程表达明显增强,说明其参与病原菌的致病性。本研究为解析尖孢镰孢菌致病基因功能分析及寄主病原互作提供了重要理论基础。     

一株兔源A型多杀性巴氏杆菌的分离鉴定和全基因组测序及分析

【背景】多杀性巴氏杆菌可导致猪肺疫、牛出血性败血症和兔出血性败血症等多种疾病,严重威胁多种动物畜牧养殖业的健康发展。【目的】重庆某兔场送检一批病死兔,为研究其病原和治疗方法,对病原进行了微生物分离和全基因组测序分析。【方法】从2022年重庆某兔场送检兔病料中进行细菌分离纯化、生化试验、16S rRNA基因鉴定、荚膜血清型分型、药敏试验和毒力基因检测,同时通过全基因组测序结果进行毒力、耐药基因注释和遗传进化等分子生物学信息分析。【结果】该菌为兔源A:ST74多杀性巴氏杆菌,命名为LXSS001,基因组序列上传到NCBI数据库(登录号为CP119523.1),药敏试验显示该菌对四环素、杆菌肽、复方新诺明和磺胺异恶唑耐药,对头孢噻肟、头孢哌酮和丁胺卡那等药物敏感。全基因组长度为2 480 671 bp,并注释到了58个毒力基因和9类药物的靶向抗药基因。通过联合建树表明其与3480株一致性最高。【结论】本研究完成了一株A型多杀性巴氏杆菌的分离鉴定和全基因组测序,并揭示了其与国内外其他分离株的进化关系,为多杀性巴氏杆菌的后续研究提供了参考依据。     

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance, but location has a less effect on maize2 homoeologs. In addition to homoeologous genes, we compared ACRs, which often harbor cis-regulatory elements, between the two subgenomes and demonstrate that maize1 ACRs have a higher level of chromatin accessibility, a lower level of sequence substitution, and are enriched in chromosomal arms. Furthermore, we find that a loss of maize1 ACRs near their nearby genes is associated with a reduction in purifying selection and expression of maize1 genes relative to their maize2 homoeologs. Taken together, our data suggest that chromatin environment and cis-regulatory elements are important determinants shaping the divergence and evolution of duplicated genes.     

A new family of CRISPR‐type V nucleases with C‐rich PAM recognition

Most CRISPR‐type V nucleases are stimulated to cleave double‐stranded (ds) DNA targets by a T‐rich PAM, which restricts their targeting range. Here, we identify and characterize a new family of type V RNA‐guided nuclease, Cas12l, that exclusively recognizes a C‐rich (5''‐CCY‐3′) PAM. The organization of genes within its CRISPR locus is similar to type II‐B CRISPR‐Cas9 systems, but both sequence analysis and functional studies establish it as a new family of type V effector. Biochemical experiments show that Cas12l nucleases function optimally between 37 and 52°C, depending on the ortholog, and preferentially cut supercoiled DNA. Like other type V nucleases, it exhibits collateral nonspecific ssDNA and ssRNA cleavage activity that is triggered by ssDNA or dsDNA target recognition. Finally, we show that one family member, Asp2Cas12l, functions in a heterologous cellular environment, altogether, suggesting that this new group of CRISPR‐associated nucleases may be harnessed as genome editing reagents.