花后高温胁迫下匀播春小麦旗叶的转录组分析

为研究不同播种模式下花后高温胁迫对春小麦旗叶转录组的影响,以宁春50号为试验材料,采用人工模拟高温的方法,设条播和匀播两种播种方式,灌水施肥方式均为水肥一体化,对高温处理后的春小麦旗叶分别构建转录组测序文库,采用FPKM法计算基因的相对表达量,并对差异表达基因进行KEGG通路分析。结果表明,相较于常温处理,高温胁迫下条播和匀播滴灌处理分别有199和1 819个基因上调表达,55和 1 335个基因下调表达,说明高温胁迫下匀播滴灌处理对春小麦旗叶转录组的表达影响明显。KEGG通路富集分析结果显示,高温胁迫下与条播滴灌处理对比,匀播滴灌处理的春小麦光合作用-天线蛋白通路注释到的差异表达基因最多,有52个,其次为淀粉和蔗糖通路（注释到50个差异表达基因）;而常温条件下与条播滴灌处理对比,匀播滴灌处理的春小麦淀粉和蔗糖代谢通路注释到的差异表达基因最多,有49个,其次为光合作用-天线蛋白通路（注释到41个差异表达基因）。因此,高温胁迫下匀播滴灌技术可以更好地改善植物的光合系统,有效缓解高温引起的小麦植株早衰。     

基于RNA-seq技术分析野生大麦穗部发育基因的表达谱及其转录动态

为明确野生大麦穗部发育过程中基因表达的动态变化,以来自以色列的野生大麦Mehula 1-2为材料,对其在穗部发育的4个关键时期（开花后3、8、13和18 d)进行RNA-seq分析,并与栽培大麦穗部的基因表达谱进行了比较。结果表明,在野生大麦穗发育的4个时间点共鉴定到17 163个基因,其中11 273个为差异表达基因,包括635个转录因子相关基因;功能富集分析表明,这些差异基因主要富集到物质合成、代谢过程、物质运输、抗逆等相关过程或通路上;野生大麦和栽培大麦穗部基因的表达谱比较分析发现,两者共同表达的基因显著富集到细胞器、催化、代谢、调节及抗逆等相关通路上,而在特异表达基因方面,栽培大麦主要集中于甲基转移酶、次生壁生物合成、核糖体蛋白等相关基因,野生大麦主要集中于逆境抗性、花青素合成、钙调蛋白等相关基因。本研究发掘的与穗部发育相关的关键基因,丰富了大麦穗部遗传改良基因资源,为进一步解析野生大麦穗部发育关键基因的表达特性和调控机制奠定了基础。     

番石榴果实品质评价及黄酮类化合物合成相关基因挖掘

【目的】综合评价番石榴Psidium guajava不同品种间的果实品质差异并挖掘黄酮类化合物合成的关键基因。【方法】对番石榴6个品种的11个果实品质指标进行测定,并结合主成分分析方法综合评价其品质差异,运用转录组测序技术比较各品种间的差异表达基因(Differentially expressed gene, DEG),通过GO和KEGG富集分析,挖掘黄酮类化合物合成的DEG,利用实时荧光定量PCR (Quantitative real-time PCR,qRT-PCR)研究DEG在不同品种间的特异性表达。【结果】6种番石榴试材中‘金斗香’和‘胭脂红’品质最优,得分较高,‘水晶’和‘西瓜红’较低,‘珍珠’和‘红宝石’居中;‘金斗香’和‘胭脂红’的类黄酮质量分数较高,分别为9.76和10.05 mg/g,是‘水晶’(5.74 mg/g)的1.5倍以上,显著高于其他品种(P>0.05)。转录组测序分析显示,‘金斗香’和‘胭脂红’的DEG聚为一类,其余4种的DEG聚为一类。黄酮类化合物的生物合成途径中CHS、FLS、CYP73A、CYP98A3、DFR、E2.1.1.104、E1.14...     

基于转录组测序分析牛不同脂肪组织的脂肪沉积差异研究

为了更好地了解肉牛(Bos taurus)的脂肪沉积机制，以安格斯牛（Aberdeen Angus）和西门塔尔牛（Simmental cattle）为模型，通过对2种脂肪组织（肾周脂肪和背皮下脂肪）进行RNA测序，确定转录组图谱。分析4个组织中共同的高表达基因，以及2个组织之间的差异表达基因。结果显示，每个样品获得约10.99 Gb数据，并注释总共23 472个基因。在50个高度表达的共同基因中，发现脂肪酸结合蛋白4（Fatty Acid Binding Protein4, FABP4），脂肪形成调节因子(Adipogenesis Regulatory Factor,ADIRF)和硬脂酰辅酶A去饱和酶(Stearoyl-CoA Desaturase,SCD)是与脂肪沉积相关的基因，表明这3个基因可能在脂肪沉积中发挥作用。在安格斯牛和西门塔尔牛的肾周脂肪与皮下脂肪组织之间分别鉴定出1 678个和1 955个差异表达基因。GO分析表明，一些DEG与代谢有关。KEGG途径分析显示，PPAR信号途径、甘油酯代谢和ECM-受体相互作用途径富集丰富。在背皮下脂肪中，PPAR信号途径和甘油脂代谢中的3个基因：视黄酸X受体α(retinoid X receptor alpha,RXRA)、C1q肿瘤坏死因子相关蛋白7(C1q and TNF related 7, C1QTNF7)和单酰甘油-O-酰基转移酶2(Monoacylglycerol O-acyltransferase 2, MOGAT2)上调；6个基因：肉碱脂酰转移酶1B(Carnitine Palmitoyltransferase 1B, CPT1B) 、解偶联蛋白1(Uncoupling Protein 1, UCP1)、 脂肪酸结合蛋白3(Fatty Acid Binding Protein 3, FABP3)、 脂肪酸转位酶(Fatty Acid Translocation enzyme, CD36) 、脂蛋白1( LPIN1) 和甘油-3-磷酸酰基转移酶3(Glycerol-3-phosphate Acyltransferase 3, GPAT3)表达量下调。在ECM-受体相互作用中，发现Ⅰ型胶原Α1(Collagen Type I alpha 1 Chain, COL1A1)、III型胶原Α1(Collagen Type III alpha 1 Chain, COL3A1) 、Ⅰ型胶原Α2(Collagen Type I alpha 2 Chain, COL1A2)和II型胶原Α1(Collagen Type II alpha 1 Chain, COL2A1)在牛的背皮下脂肪中上调，而层粘连蛋白γ3(Laminin Subunit gamma 3 , LAMC3) 和粘连蛋白γ2(Laminin Subunit gamma 2, LAMC2)的表达量下调。为验证转录组的准确性，对差异基因 COL1A1、 COL3A1、RXRA、 LPIN1和 GPAT3进行qPCR验证，结果显示qPCR结果与转录组测序数据基本一致。本研究揭示了肉牛不同脂肪组织中复杂的转录组图谱，发掘了参与脂肪沉积的候选基因。     

花魔芋响应软腐病菌侵染初期的转录组分析

为探讨花魔芋抵御软腐病害的分子机制,分别以染病初期和健康的花魔芋球茎为材料进行转录组测序。结果表明,健康和染病初期花魔芋两组出现3 222个差异表达基因,其中2 660个基因上调表达,562个基因下调表达,差异表达基因主要涉及细胞组分、生物学过程及分子功能等生理生化过程。表达量上调和下调最大的前10个基因包含编码MiAMP1抗菌蛋白、热激蛋白、胰蛋白酶与蛋白酶抑制剂、胰凝乳蛋白酶抑制剂等与抗病相关的基因。GO功能分类和KEGG通路分析表明,类黄酮和苯丙烷类物质在花魔芋抵御软腐病菌侵染初期发挥重要作用。值得关注的是,硒化合物代谢、维生素B6代谢、类黄酮生物合成、N-聚糖生物合成及链霉素生物合成通路等抗病相关的差异表达基因在花魔芋染病初期全部或大部分受诱导表达。利用高通量测序获得大量花魔芋转录组信息,有助于挖掘与花魔芋抗软腐病相关的关键基因,也为魔芋抗病分子育种提供理论参考。     

Necrotic enteritis challenge regulates peroxisome proliferator-1 activated receptors signaling and β-oxidation pathways in broiler chickens

Necrotic enteritis (NE) is an important enteric disease in poultry and has become a major concern in poultry production in the post-antibiotic era. The infection with NE can damage the intestinal mucosa of the birds leading to impaired health and, thus, productivity. To gain a better understanding of how NE impacts the gut function of infected broilers, global mRNA sequencing (RNA-seq) was performed in the jejunum tissue of NE challenged and non-challenged broilers to identify the pathways and genes affected by this disease. Briefly, to induce NE, birds in the challenge group were inoculated with 1 mL of Eimeria species on day 9 followed by 1 mL of approximately 10⁸ CFU/mL of a NetB producing Clostridium perfringens on days 14 and 15. On day 16, 2 birds in each treatment were randomly selected and euthanized and the whole intestinal tract was evaluated for lesion scores. Duodenum tissue samples from one of the euthanized birds of each replicate (n = 4) was used for histology, and the jejunum tissue for RNA extraction. RNA-seq analysis was performed with an Illumina RNA HiSeq 2000 sequencer. The differentially expressed genes (DEG) were identified and functional analysis was performed in DAVID to find protein–protein interactions (PPI). At a false discovery rate threshold <0.05, a total of 377 DEG (207 upregulated and 170 downregulated) DEG were identified. Pathway enrichment analysis revealed that DEG were considerably enriched in peroxisome proliferator-activated receptors (PPAR) signaling (P < 0.01) and β-oxidation pathways (P < 0.05). The DEG were mostly related to fatty acid metabolism and degradation (cluster of differentiation 36 [CD36], acyl-CoA synthetase bubblegum family member-1 [ACSBG1], fatty acid-binding protein-1 and -2 [FABP1] and [FABP2]; and acyl-coenzyme A synthetase-1 [ACSL1]), bile acid production and transportation (acyl-CoA oxidase-2 [ACOX2], apical sodium–bile acid transporter [ASBT]) and essential genes in the immune system (interferon-, [IFN-γ], LCK proto-oncogene, Src family tyrosine kinase [LCK], zeta chain of T cell receptor associated protein kinase 70 kDa [ZAP70], and aconitate decarboxylase 1 [ACOD1]). Our data revealed that pathways related to fatty acid digestion were significantly compromised which thereby could have affected metabolic and immune responses in NE infected birds.     

转录组技术在果树研究中的应用

介绍了转录组技术的概念及研究的技术手段,并重点综述了转录组在果树的品种鉴定、生长发育、逆境胁迫以及发现新基因等方面的研究进展,及其在果树上的应用前景。     

朱顶红转录组De novo数据及功能注释分析

本研究利用Illumina高通量测序技术对PP333处理的朱顶红进行了RNA-seq测序,共获得26.91 Gb的数据,对其进行过滤去冗余后得到Unigene 106 684个,总长度为92 002 803 bp,平均长度为862 bp,N50为1 494 bp,GC含量为42.47%,Q20均达98%以上,表明测序质量较好。根据七大功能数据库比对结果,分别有53 853 (NR:50.48%)、29 732 (NT:27.87%)、35 889 (SwissProt:33.64%)、42 221 (KOG:39.58%)、40 258(KEGG:37.74%)、12 186 (GO:11.42%)以及42 559 (InterPro:39.89%)个Unigene获得功能注释。根据Nr注释结果,可匹配到物种为油棕、海枣、小果野芭蕉、莲等。在KOG注释中通用功能和预测占比最高。按GO功能分类,可分为生物过程、细胞组成、分子功能三类,52个分支,大量Unigene与代谢过程、细胞过程及单生物过程相关。按照KEGG功能分类,分为6类,21个功能组,大量Unigene与代谢相关,占比60.39%。本研究结果为朱顶红的矮化机理研究及其基因挖掘提供依据。     

Gene response in rice plants treated with continuous fog influenced by pH,was similar to that treated with biotic stress

Background

Throughout Asia, including Japan, rice plants are cultivated in a wide range of areas from lowlands to highlands and are frequently exposed to fog, including acid fog. Some physiological studies have shown that acid fog can be a stress factor for plants. We analyzed the gene expression profiles of rice plants treated with artificially prepared simulated acid fog (SiAF) or simulated neutral fog (SiNF) for 1 or 7 days.

Results

Microarray analysis results suggested that both the SiAF and the SiNF treatments induced the expression of genes involved in the defense and stress responses in rice plants. Induction of such genes was detected in plants treated with SiAF for 1 day, and the number of induced genes increased in plants treated with SiAF for 7 days. The genes for defense and stress responses were also induced by SiNF for 7 days, although they were not induced by SiNF for 1 day. The gene expression profiles of the SiAF-treated and the SiNF-treated plants were compared to those of plants treated with other stress factors. The comparison revealed that both SiAF and SiNF treatments have similar effects to biotic stresses and ozone stress. The genes encoding NADPH oxidase and germin, which function in apoplasts, were also induced by SiAF, SiNF and biotic stresses.

Conclusions

These findings suggest that both the SiAF and the SiNF treatments may result in oxidative stress through the apoplastic production of reactive oxygen species.