蕈菌基因组测序的进展

蕈菌在人类社会和自然界扮演重要角色,除了食用和药用价值以外很大的前景是应用于碳源回收和生物环境修复方面。随着高通量测序技术的广泛应用,蕈菌的基因组测序得以实现,而蕈菌的基因组测序工作将极大地促进蕈菌基础生物学研究,同时为珍稀物种的保育提供科学依据。在蕈菌基因组测序中,美国能源部所属的联合基因组研究所做了大量工作,尤其是其"1 000 Fungal Genomes"项目。文中在概括介绍蕈菌全基因组测序的检索方法、测序技术和基因组测序类型基础上,通过文献调查和数据库检索收录了323种已完成或部分完成基因组测序的蕈菌(分属于70个科,其中有8个物种科级单位不确定),为大型食药用菌的遗传多样性的分析和保护生物学研究提供参考资料。     

小单孢菌(Micromonospora wenchangensis DSM 45709)全基因组测序及分析

小单孢菌(Micromonospora wenchangensis)DSM45709是一种高GC含量的革兰氏阳性放线菌,分离自中国海南文昌红树林沉积物。目前,还没有相关研究报道Micromonospora wenchangensis的全基因组序列,这限制了其代谢产物合成途径和比较基因组学的研究。本研究通过高通量测序技术对小单孢菌DSM45709进行全基因组测序,使用Velvet软件进行组装拼接得到150个Contigs,整个基因组大小约7.51 Mb,GC含量为73.04%,序列已提交至给GenBank数据库,登录号为MZMV00000000。本研究同时对基因组序列进行了基因预测与功能注释、COG和GO聚类分析及次级代谢产物合成基因簇预测等,相关研究结果将为小单孢菌Micromonospora wenchangensis的功能基因组学研究提供基础数据。     

小单孢菌(Micromonospora rifamycinica)AM105全基因组测序及分析

小单孢菌(Micromonospora rifamycinica)AM105是一种高GC含量的革兰氏阳性放线菌,分离自中国南海红树林沉积物,能够合成利福霉素类抗生素。目前,还没有相关研究报道Micromonospora rifamycinica的全基因组序列,这限制了代谢产物合成途径和比较基因组学等研究。本研究首次通过高通量测序技术对小单孢菌AM105进行全基因组测序,使用Velvet软件进行组装拼接得到388个Contigs,整个基因组大小约6.85 Mb,GC含量为73.1%,序列已提交至美国国立生物技术信息中心(NCBI)的Gen Bank数据库(LRMV01000000)。本研究同时对基因组序列进行了基因预测与功能注释、COG和GO聚类分析及次级代谢产物合成基因簇预测等,相关研究结果将为小单孢菌Micromonospora rifamycinica的功能基因组学研究提供基础数据。     

基于高通量测序的植物群体基因组学研究进展

作为群体遗传学一种新的表现形式,群体基因组学是将基因组概念和技术与群体遗传学理论体系相结合,通过覆盖全基因组范围内的多态位点的分布式样推测位点特异性效应和全基因组效应,从而提升人们对微进化的理解。近年来,随着第二代高通量测序技术的出现和改进,完成基因组测序的植物种类迅速增加,大规模的重测序也随之开展。与此同时,在一些尚未完成基因组测序的植物物种中,也开展了一些平行测序。这些重测序和平行测序极大地促进了群体基因组学的发展,加深了人们对相关植物种群在基因组水平上的遗传多样性、连锁不平衡水平、选择作用、群体历史及复杂性状的分子机理等群体基因组学方面的认识。本文简要介绍了群体基因组学的概念、研究方法等,重点综述了基于高通量测序的植物群体基因组学的研究动态,展望了植物群体基因组学的发展前景并讨论了存在的问题,以期为相关研究提供借鉴和参考。     

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...     

家蚕miRNA研究获新进展

MicroRNAs（miRNAs）作为转录后基因表达的一个重要的调控因子,参与了包括发育、代谢、疾病的发生等各种重要的生理过程。家蚕基因组的测序完成为在全基因组水平鉴定家蚕miRNAs以及与其他昆虫进行比较基因组学研究提供了契机。     

基于流式细胞术和K-mer分析的银缕梅属(Parrotia C.A.Mey.)植物基因组大小测定

金缕梅科(Hamamelidaceae)银缕梅属(Parrotia C.A.Mey.)仅包含银缕梅(Parrotia subaequalis(H.T.Chang)R.M.Hao&H.T.Wei)和波斯铁木(Parrotia persica(DC.)C.A.Mey.)两种落叶阔叶乔木,其中银缕梅是我国华东地区特有的Ⅰ级濒危珍稀保护植物,属东亚第三纪孑遗成分;其姊妹种波斯铁木则间断分布于伊朗北部,属北极第三纪孑遗植物类群。本研究首次利用流式细胞术和K-mer分析方法对银缕梅属两姊妹种的基因组大小进行了测定,建立和优化了以萝卜(Raphanus sativus L.‘Saxa’)为内标、WPB(Woody plant buffer)为细胞核解离液的两种植物单倍体基因组的DNA含量(DNA C值)流式测定的适宜体系,旨在为金缕梅科银缕梅属植物的全基因组测序、基因组学研究、种质资源开发和利用以及物种保育等提供前期基础数据参考;同时也可为金缕梅科其他属、种的基因组大小测定提供借鉴。主要研究结果如下:(1)通过流式测定银缕梅基因组大小约为971.45±13.91 Mb,波斯铁木基因组大小约为890.52±24.69 Mb;(2)K-mer分析估测银缕梅基因组大小为951.70 Mb,杂合率为1.740%,重复序列比例为77.50%;波斯铁木基因组大小为858.50 Mb,杂合率为0.695%,重复序列占74.30%;(3)银缕梅属于高杂合和高重复基因组,波斯铁木则属于微杂合和高重复基因组。本研究的结果为银缕梅属植物后续基于DNA三代高通量测序技术的全基因组测序、组装及去冗余处理等工作提供了重要的数据参考。     

小单孢菌(Micromonospora rosaria)DSM803全基因组测序及分析

小单孢菌(Micromonospora rosaria)DSM 803是一种高GC含量的革兰氏阳性放线菌,分离自美国德克萨斯州土壤,能够合成玫瑰霉素抗生素。目前,还没有相关研究报道Micromonospora rosaria的全基因组序列,这限制了代谢产物合成途径和比较基因组学等研究。本研究首次通过高通量测序技术对小单孢菌DSM803进行全基因组测序,使用Velvet软件进行组装拼接得到310个Contigs,整个基因组大小约7.38 Mbp,GC含量为73.4%,序列已提交至美国国立生物技术信息中心(NCBI)的Gen Bank数据库(LRQV00000000)。比较基因组学及玫瑰霉素合成途径相关基因分析结果显示:小单孢菌DSM 803在碳水化合物转运和代谢及信号转导功能方面要明显强于其它功能;玫瑰霉素生物合成基因簇由20个基因组成并分散于4个Contigs中。本研究首次报道了一株大环内酯类抗生素玫瑰霉素生产菌小单孢菌DSM 803的全基因组序列,分析了基因组基本特征,预测了次级代谢产物合成基因簇,探讨了玫瑰霉素生物合成途径,为后续的进一步代谢调控与合成生物学提供了理论基础。     

林木基因组学研究进展

林木基因组学研究进展迅速。结构基因组学方面,已构建了近40个主要造林树种的遗传连锁图谱,在不同树种中定位了30余个重要的数量性状位点,在部分树种中开展了基因组比较和综合图谱构建研究,杨树的全基因组测序已经完成,桉树的全基因组测序正在进行。功能基因组学方面,已分析了主要造林树种多种组织的转录组EST序列,对林木次生生长与木材形成、开花和抗寒性的形成等过程开展了功能基因组学研究。另外,探讨了林木基因组学研究的发展趋势,以期为我国林木基因组学研究提供有益的参考。     

一株新的沙门菌烈性噬菌体IME-SAL1的分离、全基因组测序和比较基因组分析

目的:分离鉴定一株沙门菌的烈性噬菌体,观察其形态大小,完成全基因组测序,分析其基因组结构和进化关系,为治疗沙门菌感染提供新的策略和实验依据。方法:以沙门菌SAL95作为指示菌从医院废水中分离噬菌体,分离到的噬菌体经浓缩和纯化后采用透射电镜观察其形态大小,提取噬菌体的基因核酸并完成全基因组高通量测序,分析其全基因组的结构特征,通过比较基因组分析研究其进化关系。结果:从解放军307医院未经消毒处理的废水中分离到一株烈性沙门菌噬菌体。电镜观察显示,该噬菌体头部呈立体对称,有一不收缩的长尾。其基因组全长113 183 bp,比较基因组分析确定该噬菌体为一株新的沙门菌噬菌体,命名为IME-SAL1。结论:从医院废水中分离到一株烈性沙门菌噬菌体IME-SAL1,研究了该噬菌体的分类、基因组结构、进化关系,可为其实际应用提供参考。     

Cloning and characterization of squalene synthase (SQS) gene from Ganoderma lucidum

This report provides the complete nucleotide sequences of the full-length cDNA encoding squalene synthase (SQS) and its genomic DNA sequence from a triterpene-producing fungus, Ganoderma lucidum. The cDNA of the squalene synthase (SQS) (GenBank Accession Number: DQ494674) was found to contain an open reading frame (ORF) of 1,404 bp encoding a 468-amino-acid polypeptide, whereas the SQS genomic DNA sequence (GenBank Accession Number: DQ494675) consisted of 1,984 bp and contained four exons and three introns. Only one gene copy was present in the G lucidum genome. The deduced amino acid sequence of Ganoderma lucidum squalene synthase (Gl-SQS) exhibited a high homology with other fungal squalene synthase genes and contained six conserved domains. A phylogenetic analysis revealed that G. lucidum SQS belonged to the fungi SQS group, and was more closely related to the SQS of U. maydis than to those of other fungi. A gene expression analysis showed that the expression level was relatively low in mycelia incubated for 12 days, increased after 14 to 20 days of incubation, and reached a relatively high level in the mushroom primordia. Functional complementation of Gl-SQS in a SQS-deficient strain of Saccharomyces cerevisiae confirmed that the cloned cDNA encoded a squalene synthase.     

The arbuscular mycorrhizal fungus Glomus intraradices is haploid and has a small genome size in the lower limit of eukaryotes

The genome size, complexity, and ploidy of the arbuscular mycorrhizal fungus (AMF) Glomus intraradices was determined using flow cytometry, reassociation kinetics, and genomic reconstruction. Nuclei of G. intraradices from in vitro culture, were analyzed by flow cytometry. The estimated average length of DNA per nucleus was 14.07+/-3.52 Mb. Reassociation kinetics on G. intraradices DNA indicated a haploid genome size of approximately 16.54 Mb, comprising 88.36% single copy DNA, 1.59% repetitive DNA, and 10.05% fold-back DNA. To determine ploidy, the DNA content per nucleus measured by flow cytometry was compared with the genome estimate of reassociation kinetics. G. intraradices was found to have a DNA index (DNA per nucleus per haploid genome size) of approximately 0.9, indicating that it is haploid. Genomic DNA of G. intraradices was also analyzed by genomic reconstruction using four genes (Malate synthase, RecA, Rad32, and Hsp88). Because we used flow cytometry and reassociation kinetics to reveal the genome size of G. intraradices and show that it is haploid, then a similar value for genome size should be found when using genomic reconstruction as long as the genes studied are single copy. The average genome size estimate was 15.74+/-1.69 Mb indicating that these four genes are single copy per haploid genome and per nucleus of G. intraradices. Our results show that the genome size of G. intraradices is much smaller than estimates of other AMF and that the unusually high within-spore genetic variation that is seen in this fungus cannot be due to high ploidy.     

Influence of culture parameters on paper mill effluent decolourization by a white rot fungus Ganoderma lucidum

Efficacy of a white rot fungus G. lucidum for reduction of colour of paper mill effluent under various growth conditions was evaluated. G. lucidum cultured in IBME medium supported maximum colour reduction on 18th day of fungal growth. The optimization of growth parameters further improved colour reduction. The 18 day old culture at 4 g/l inoculum concentration resulted in maximum decolourization (89%) of the effluent with pH adjusted to 6.5 at 35 degrees C along with maximum reduction in biological oxygen demand and chemical oxygen demand. Relative contribution of lignin peroxidase and laccase to the decolourization of paper mill effluent by G. lucidum was also observed.     

Whole-genome survey and phylogenetic analysis of Gadus macrocephalus

Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.     

稻曲病菌UV-2菌株细菌人工染色体文库构建及分析

【目的】稻曲病(Rice false smut)是由稻曲病菌[Villosiclava virens (Cooke) Tak.]引起的严重危害水稻的真菌病害。构建稻曲病菌UV-2的大片段DNA细菌人工染色体(Bacterial artificial chromosome, BAC)文库, 为致病相关基因的鉴定及在图位克隆、比较基因组学等方面的研究奠定基础。【方法】以幼嫩菌丝为材料制备大分子基因组DNA包埋块, 用Hind III部分酶解后经脉冲凝胶电泳筛选, 回收大片段DNA并与pIndigoBAC536-S 载体连接, 连接产物转化大肠杆菌菌株DH10B T1 Phage-Resistant 细胞后进行蓝白斑筛选, 白色菌落捡入384孔板置于?80 °C低温保存。【结果】成功构建UV-2菌株的高质量、高覆盖度的BAC文库, 该文库共含10 368个克隆, 平均插入片段为124.4 kb, 空载率小于1%, 约覆盖该菌基因组的36.8倍。【结论】克服了真菌大分子基因组DNA制备难控制的技术难题, 建立了首个稻曲病菌的BAC文库。该文库已作为一种公共基因组资源向研究者开放(http://GResource.hzau.edu.cn)。     

灵芝(Ganoderma lucidum)漆酶基因的克隆及其序列分析

漆酶(laccase EC1·10·3·2)是一种含Cu的多酚氧化酶,自从1883年日本学者吉田首次从漆树汁液中发现以来,漆酶特别是真菌漆酶一直是生物学、化学和环境科学等领域十分活跃的研究热点,在纸浆的生物漂白[1,2],有毒污染物的降解[3~5]等方面有较大的应用价值.根据其来源主要分为漆树漆酶和真菌漆酶两大类,由一个结构相似的基因家族所编码,目前,至少有40个以上的真菌漆酶基因被克隆和测序[6~9],最近也有从细菌中克隆到漆酶基因的报道[10~12].我国幅员辽阔,具有十分丰富的真菌资源,但是我国对漆酶的研究与发达国家相比还十分落后,对于漆酶基因资…     

A Polymer Model for the Structural Organization of Chromatin Loops and Minibands in Interphase Chromosomes

A quantitative model of interphase chromosome higher-order structure is presented based on the isochore model of the genome and results obtained in the field of copolymer research. G1 chromosomes are approximated in the model as multiblock copolymers of the 30-nm chromatin fiber, which alternately contain two types of 0.5- to 1-Mbp blocks (R and G minibands) differing in GC content and DNA-bound proteins. A G1 chromosome forms a single-chain string of loop clusters (micelles), with each loop ~1–2 Mbp in size. The number of ~20 loops per micelle was estimated from the dependence of geometrical versus genomic distances between two points on a G1 chromosome. The greater degree of chromatin extension in R versus G minibands and a difference in the replication time for these minibands (early S phase for R versus late S phase for G) are explained in this model as a result of the location of R minibands at micelle cores and G minibands at loop apices. The estimated number of micelles per nucleus is close to the observed number of replication clusters at the onset of S phase. A relationship between chromosomal and nuclear sizes for several types of higher eukaryotic cells (insects, plants, and mammals) is well described through the micelle structure of interphase chromosomes. For yeast cells, this relationship is described by a linear coil configuration of chromosomes.     

雷公藤解毒持效双向发酵工艺的建立

采用双向发酵的原理,运用"发酵过程动态比较法"研究了灵芝接种于雷公藤药性基质上发酵不同时间所得菌质的化学成分、急性毒性和免疫功能的变化,以其确定雷公藤解毒持效双向发酵的最佳发酵终点。研究结果表明:发酵第30天所得的菌质(G30)总二萜的含量最低,为0.57%;与雷公藤生药比较,G30的LD50最高,且发酵第30天所得菌质的体液免疫和细胞免疫抑制作用最强。综合对成分含量、毒性及药效的动态数据联系比较、分析,确定了雷公藤解毒持效双向发酵的发酵终点与适宜的发酵周期是菌丝长满瓶后的第30天。