糙皮侧耳乙醛脱氢酶基因PoALDH1的克隆与非生物胁迫下的表达分析

本研究从糙皮侧耳中克隆了乙醛脱氢酶基因PoALDH1(Gen Bank登录号为KT026035)和其全长c DNA序列。长为2 016bp的PoALDH1序列编码478个氨基酸,分子量约为52k Da,氨基酸序列中含有乙醛脱氢酶保守的谷氨酸活性位点和半胱氨酸残基活性位点。PoALDH1基因在大肠杆菌中表达后显示,重组菌株的乙醛脱氢酶比活力为0.58U/mg,且重组菌株的乙醛耐受性显著高于对照菌株。实时荧光定量PCR(quantitative real-time PCR)分析PoALDH1基因在糙皮侧耳不同发育时期的表达结果显示,PoALDH1基因在原基期的表达量约为双核菌丝期的5倍。PoALDH1基因在原基发育起始阶段经光照及温差刺激后均上调表达。当糙皮侧耳菌丝暴露在不同浓度的氯化钠及甘露醇的条件下时,菌丝生长均受到抑制且PoALDH1基因的表达量均高于对照。研究结果将为进一步从分子水平揭示糙皮侧耳的抗逆机制以及食用菌的发育奠定一定基础。     

原生质体再生对糙皮侧耳Pleurotus ostreatus病毒脱除的效果

以糙皮侧耳Pleurotus ostreatus菌株新831和豫6为材料,从这两个菌株的菌丝体中提取了糙皮侧耳病毒基因组,共有3个dsRNA片段,大小分别为8.2kb、2.6kb和1.1kb。采用菌丝尖端分离脱毒、原基组织分离脱毒和原生质体再生脱毒技术对糙皮侧耳菌丝体进行脱毒处理,利用dsRNA技术对脱毒效果进行检测。结果显示,原基组织分离脱毒后3个条带依然存在;菌丝尖端分离脱毒后,8.2kb和1.1kb 2个条带完全脱除,2.6kb的条带亮度有所减弱;原生质体再生脱毒后3个条带完全脱除;对3种脱毒技术得到的菌株进行生理生化指标测定,结果显示,原生质体再生脱毒菌株的菌丝生长速度、生物量、呼吸强度、纤维素酶活等均明显优于出发菌株、原基组织分离脱毒和菌丝尖端分离脱毒菌株;栽培结果表明,原生质体再生脱毒菌株前两茬菇的生物学效率达到96.4%－99.1%,比出发菌株提高19.9%－25.4%,并且菌盖宽度和长度有所增加,表明原生质体再生技术可以有效脱除糙皮侧耳菌株病毒,提高糙皮侧耳栽培产量。     

糙皮侧耳乳酸脱氢酶鉴定及其菌丝高温胁迫下表达特征分析

乳酸脱氢酶（lactate dehydrogenase,LDH）可催化丙酮酸与乳酸（lactic acid,LA）之间的可逆转化，为探索乳酸脱氢酶基因在糙皮侧耳（Pleurotus ostreatus）菌丝体高温胁迫响应中的作用，在糙皮侧耳（P. ostreatus）菌株CCMSSC00389基因组中鉴定获得了8个乳酸脱氢酶编码基因。生物信息学分析结果显示，3个基因编码D型乳酸脱氢酶，5个基因编码L型乳酸脱氢酶。氨基酸序列比对、系统发育、三维结构和亚细胞定位分析显示，3个D型乳酸脱氢酶的同源性较高，可能属于细胞色素C依赖的D型乳酸脱氢酶，D-LDH2和D-LDH3位于线粒体中；5个L型乳酸脱氢酶的氨基酸序列同源性较低，并按电子受体和亚细胞定位的不同分为3个类型。通过检测36℃、40℃高温胁迫下乳酸脱氢酶基因的表达量变化，明确D-ldh3、L-ldh5和L-ldh7表达特征相同，L-ldh6和L-ldh8的表达特征相同，D-ldh1、D-ldh2和L-ldh4则表现出不同的基因表达趋势，表明乳酸脱氢酶基因对不同高温胁迫温度的响应方式存在差异。高温胁迫条件下，乳酸脱氢酶总酶活性降低，胞内乳...     

糙皮侧耳不同单核体基因序列的保守性分析

从已公布的糙皮侧耳基因组信息入手,用全局比对法计算两个不同单核之间基因序列的相似性,这种相似性与基因序列的保守性有关。通过对保守和不保守的基因集合进行功能富集分析研究,分析与序列保守性相关的Gene Ontology功能。保守基因集合中显著富集的主要是一些代谢过程、催化酶活性、输送等功能。不保守基因集合中显著富集的多为激酶活性、绑定、调控等功能。     

机械损伤对糙皮侧耳原基形成的影响

原基期是糙皮侧耳Pleurotus ostreatus发育进程的关键时期。本研究以糙皮侧耳菌株New 831为试验材料,通过对糙皮侧耳菌丝机械损伤,探讨机械损伤对糙皮侧耳原基诱发的影响。菌丝满板后,经过机械损伤处理,到原基期每隔4d取样一次,测定了这些样品处理组与对照组的活性氧及脂质过氧化水平,并且通过荧光定量分析了Po.WC-1、Po.WC-2、fst3和fst4基因的表达量。结果表明：机械损伤组和对照组的活性氧水平随时间的增加均呈现“先升后降”的趋势,机械损伤总体提高了活性氧的水平,并且机械损伤导致原基提前形成,表明活性氧水平的提高,可能促进了糙皮侧耳原基形成;荧光定量分析发现糙皮侧耳菌丝机械损伤处理后,Po.WC-1、Po.WC-2、fst3、fst4基因的表达量均发生变化,这些基因的变化表明它们可能参与调控糙皮侧耳原基形成;Po.WC-2和fst3基因在第8天时的显著上调表达可能促进了糙皮侧耳原基形成。研究结果表明机械损伤能够促进糙皮侧耳原基提前形成,这将为进一步研究原基形成过程中机械损伤的作用机制奠定基础。     

一种快速辨别糙皮侧耳和肺形侧耳的方法

目的：建立一种快速、经济的方法辨别糙皮侧耳（P.ostreatus）和肺形侧耳（P.pulmonarius）。方法：在GenBank下载糙皮侧耳和肺形侧耳的ITS序列,经ClustalX序列比对,利用Primer 3设计特异引物组合1F（5′-GATAGATCTGTGAAGTCGTC-3′）、1R（5′-TCACAATTGGAAAGAAACC-3′）和2R（5′-TGCGTGCTATTGATGAGTGA-3′）,最后经PCR扩增和琼脂糖凝胶电泳检测。结果：5个糙皮侧耳菌株均能得到2条带,分别为342bp和459bp。4个肺形侧耳菌株均能扩增到一条446bp的片段。结论：该组引物适合辨别糙皮侧耳和肺形侧耳。     

球孢白僵菌种内比较线粒体基因组学分析

【目的】明确球孢白僵菌种内线粒体基因组的分化程度。【方法】从GenBank下载已知的球孢白僵菌6个菌株线粒体基因组序列,详细分析基因组的组成结构,比较外显子区、内含子区和基因间区的碱基变异情况,分析菌株间的系统发育关系。【结果】球孢白僵菌不同菌株的线粒体基因组大小为28.8–32.3 kb,都有14个常见的核心蛋白编码基因、2个rRNA基因和25个tRNA基因,具有很强的共线性关系。但是,不同菌株含有的线粒体内含子数目存在差异(2–5个/菌株),在cox1、cox2和nad1基因中表现出内含子插入/缺失多态性,这是导致线粒体基因组大小变化的主要因素。对外显子、内含子和基因间区的碱基变异情况进行分析,发现内含子和基因间区相对变异较大,而外显子区相对变异较小。系统发育分析发现,这些球孢白僵菌菌株以很高的支持度聚在一起,具有相同内含子分布规律的菌株也具有较近的聚类关系。【结论】本研究首次报道球孢白僵菌因内含子数目不同、插入缺失突变和单核苷酸变异等在线粒体基因组上表现出较大程度的遗传分化,为认识真菌种内线粒体基因组分化提供了新的证据。     

肺形侧耳线粒体基因组多态性鉴定

线粒体是能量转化与ATP形成的重要场所,已有多种食用真菌的线粒体基因组被相继组装注释,但肺形侧耳的线粒体基因组鲜有报道。本研究对野生肺形侧耳X2菌株的线粒体基因组进行组装并注释,由野生菌株X2与主栽菌株JX线粒体大片段差异序列,构建分子标记来鉴别野生和主栽肺形侧耳菌株。结果显示X2的线粒体基因组为大小75 709bp的闭合环状结构,含有rRNA的大小亚基基因,25个负责携带氨基酸的tRNA基因以及14个常见蛋白编码基因,在cox1基因上含有9个内含子。内含子主要为IB型,包含LAGLIDADG_1 superfamily、GIY-YIG_Cterm superfamily保守结构域。位于菌株X2与JX内含子和基因间区上的大片段差异序列,是造成种内线粒体多态性的主要因素。根据两菌株的差异片段构建系统进化树的结果显示,内含子、rnl-trnX、trnD-atp6序列能够将两株野生菌株和其他主栽菌株区分开,可用于野生肺形侧耳种内鉴定,而且trnD-atp6效果最佳。     

糙皮侧耳脲酶基因的克隆和原核表达分析

尿素是现代农业生产中应用较为广泛的一种氮素化肥,而脲酶（EC 3.5.1.5）是尿素分解利用的关键酶。本文以糙皮侧耳Pleurotus ostreatus栽培菌株New 831为试验材料,探究了糙皮侧耳对尿素的利用情况,结果表明：糙皮侧耳可利用尿素作为唯一氮源,平板培养时尿素最适添加量为20mmol/L;在液体摇瓶培养过程中,培养液中的铵根浓度表现为先急剧升高后缓慢降低。通过对P. ostreatus PC15菌株基因组分析,获得了一个功能注释为脲酶的基因,并克隆获得了其全长基因组DNA（gDNA）和编码区（CDS）片段,命名为Pourease。结果表明：Pourease基因的gDNA和CDS长度分别为3 003bp和2 517bp,由10个外显子和9个内含子组成;Pourease蛋白由838个氨基酸组成,预测分子量为90.03kDa,与SDS-PAGE分析结果相符;Pourease蛋白与细菌、真菌和植物来源的脲酶具有52%-82%的一致性,且含有脲酶保守的镍离子结合位点;与洋刀豆脲酶空间结构类似,Pourease蛋白也以同源三聚体的形式存在。     

三种侧耳属真菌基因组密码子偏好性比较分析

为了解3种侧耳属真菌基因组密码子的使用偏性及影响因素,本研究以糙皮侧耳、刺芹侧耳和白灵侧耳基因组CDS序列为研究对象,通过生物信息学方法对3种侧耳密码子使用偏性进行了分析。结果表明,3种侧耳基因组总碱基组成差异小,GC含量高。RSCU、RFSC分析表明糙皮侧耳G/C结尾的偏好密码子的比例最高(82.14%),并且有3个特有偏好密码子。3种侧耳共有偏好密码子25个,以G/C结尾的占80%;共有高频密码子3个,均以G/C结尾。密码子相似性分析表明3种侧耳密码子使用模式比较相似(相似性指数均小于0.001),其中刺芹侧耳与白灵侧耳的相似性最高(相似性指数为0.000259014);且3种侧耳密码子的使用频率与灰盖鬼伞和金针菇较为接近。PR2-plot、ENc-GC3和中性绘图分析表明3种侧耳密码子偏好性使用主要受自然选择影响,在一定程度上也受碱基突变压力和其他因素影响。上述结论为分析侧耳真菌的进化规律及选择最佳异源表达受体系统提供了依据。     

Identification of genome-wide variations among three elite restorer lines for hybrid-rice

Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice.     

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.     

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by threefold in the marine teleost Chrysophrys auratus

Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied nonmodel species in the wild. As part of our long‐term research programme on the nonmodel teleost fish Australasian snapper (Chrysophrys auratus), we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and inversions) in fishes and evaluate overlap of genomic variants with regions under putative selection (Tajima's D and π), and coding sequences (genes). For this, we analysed six males and six females from three locations in New Zealand and generated a high‐resolution genomic variation catalogue. We characterized 20,385 SVs and found they intersected with almost a third of all annotated genes. Together with small indels, SVs account for three times more variation in the genome in terms of bases affected compared to SNPs. We found that a sizeable portion of detected SVs was in the upper and lower genomic regions of Tajima's D and π, indicating that some of these have an effect on the phenotype. Together, these results shed light on the often neglected genomic variation that is produced by SVs and highlights the need to go beyond the mere measure of SNPs when investigating evolutionary processes, such as species diversification and adaptation.     

Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family

Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR–ESTs could be assigned a significant match to the protein database. 3037 unique SSR–FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.     

Multiple large segment deletion method for Corynebacterium glutamicum

A precise and scarless genome excision method, employing the Cre/loxP system in concert with double-strand break (DSB)-stimulated intramolecular recombination was developed. The DSBs were mediated by the restriction endonuclease, I-SceI. It permitted multiple deletions of independent 14-, 43-, and 10-kb-long genomic regions on the Corynebacterium glutamicum genome. Accuracy of deletion was confirmed by the loss of marker genes, PCR, and sequencing of new genome joints. Eleven, 58, and 4 genes were predicted on the 14-, 43-, and 10-kb deleted regions, respectively. Although the resultant mutant lost a total of 67 kb encoding 73 genes, it still exhibited normal growth under standard laboratory conditions. Such a large segment deletion method in which multiple, successive deletions are possible is useful for genome engineering.     

RNA-seq用于获得共轭亚油酸对贵妃鸡肌内脂肪代谢调控的关键基因

通过转录物组测序获得在贵妃鸡基础日粮中添加共轭亚油酸(CLA)对肌内脂肪代谢的差异表达基因,经生物信息学分析获得相关的信号通路及可能发挥重要作用的候选基因,为CLA对肌内脂肪沉积的分子机制奠定基础。本研究选用55日龄健康的贵妃鸡为试验动物,在基础日粮中添加CLA 0%、1%和2%,预饲期1周,正饲期6周。屠宰采集胸肌组织进行转录物组测序,对测序数据进行差异表达分析,差异表达基因GO功能和差异表达基因KEGG通路富集分析,筛选出与胸肌脂类代谢相关的差异表达基因,利用qRT-PCR对差异表达基因进行验证。结果显示,共获得1 065个差异表达基因,其中上调基因703个,下调基因362个。GO富集结果显示,差异表达基因主要富集在生物过程的细胞过程、单一生物过程、生物调节和代谢过程。KEGG信号通路富集显示,差异表达基因显著富集在黏着斑、不饱和脂肪酸生物合成、脂肪酸生物合成和类固醇生物合成等信号通路中,发现11个主要与肌内脂肪代谢相关的候选基因,分别是FADS1、FADS2、ELOVL5、ACOX2、SLC27A1、FABP5、LPL、LOC107050163、ENSGALG00000030996、ENSGALG00000005043和ENSGALG00000048882。并随机选取6个基因进行qRT-PCR验证,其相对表达量变化趋势与测序结果一致。本研究筛选到CLA影响贵妃鸡胸肌脂类代谢相关的差异表达基因,并对11个主要参与脂肪代谢相关的基因进行分析,为揭示CLA调控肌内脂肪沉积的分子机制奠定基础。     

Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines

Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.     

不同大小规格墨西哥湾扇贝(Argopecten irradians concentricus)转录组分析及生长相关基因筛选

墨西哥湾扇贝(Argopecten irradians concentricus)是中国双壳贝类养殖的重要经济品种,具有较高的研究价值,然而,转录组学及基因组学信息的匮乏,严重制约了该贝的遗传改良进程。本研究基于Illumina Hi SeqTM2000平台,对5月龄大规格(平均体质量16.05 g)和小规格(平均体质量5.57 g)墨西哥湾扇贝进行转录组测序,经de nove组装,大、小规格墨西哥湾扇贝分别获得120 563和118 794条高质量unigenes,unigene的平均长度分别为944 bp和969 bp;按照FDR≤0.001且|log2Ratio|≥1的原则,共筛选出9 901个差异表达基因,其中,大规格组相对于小规格组,上调基因4 976个(50.26%),下调基因4 925个(49.74%);六大公共数据库Blast比对结果显示,差异表达基因在Nr数据库的注释率最高,其次是GO数据库;从已获功能注释的差异表达基因中筛选得到47个生长相关候选基因,涉及多个生长因子及其受体;GO功能富集结果显示,膜、L-氨基酸运输和糖基键水解酶活性分别是细胞组分、生物过程和分子功能富集unigene最多的条目;Pathway富集分析发现,3 699条差异表达基因被成功注释到252条代谢通路中,其中33条为显著性富集通路(p<0.05),富集度最高的是焦点粘附;大规格组中共鉴定出10 870个SSRs和242 551个SNPs,小规格组中共鉴定出10 857个SSRs和228 121个SNPs。研究结果为墨西哥湾扇贝分子标记批量开发、功能相关基因挖掘以及分子遗传育种提供了理论数据支撑。     

Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB-1 reveals how magnetosome synthesis developed

The entire structure of a 98 kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98 kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region has the characteristics of a genomic island: low GC content, location between two repetitive sequences, and the presence of an integrase in the flanking region of the first repetitive sequence. This 98 kb genomic region has the potential for transfer by the integrase activity. Comparative genome analysis revealed other regions with a high concentration of orthologs in magnetic bacteria besides the 98 kb region, and magnetosome synthesis seemed to need not only the exogenous 98 kb region, but also other orthologs and individually originating genes.