侧孢短芽孢杆菌S2-31拮抗下细辛叶枯病菌转录组差异表达分析

通过分析侧孢短芽孢杆菌拮抗作用下叶枯病菌的转录组学特征,研究差异表达基因(DEGs)和代谢通路的富集情况,初步探索侧孢短芽孢杆菌拮抗叶枯病菌的分子机制。首先利用S2-31与叶枯病菌的对峙培养观察其拮抗作用,然后利用转录组测序探究侧孢短芽孢杆菌拮抗下和正常生长下的叶枯病菌的基因表达水平差异,并进行RT-qPCR验证,最后,利用相关数据库对DEGs进行注释和富集分析。对峙培养后,叶枯病菌菌丝出现皱缩、扭曲等现象。测序后共得到3681个DEGs,其中2224个相对上调,1457个相对下调。GO功能注释分析表明,上调和下调表达的DEGs均注释到生物过程8个亚群、细胞组分8个亚群和分子功能4个亚群。KEGG富集分析中,共有732个unigenes定位到115条生物学通路中,其中富集程度相对较高的通路有氨基糖和核苷糖代谢、糖基磷脂酰肌醇(GPI)锚定生物合成和过氧化物酶体;涉及差异基因较多的通路有淀粉和蔗糖代谢、剪接体和胞吞作用;上调表达的DEGs主要富集在代谢途径,下调表达的DEGs主要富集在遗传信息处理和细胞过程途径。从显著富集的通路中筛选出与菌丝生长发育相关的差异表达基因,结果表明侧孢短芽孢杆菌主要抑制病原菌菌丝过氧化物酶体的形成、胞吞过程和GPI锚定的合成等过程。差异表达基因的RT-qPCR验证结果与转录组测序的结果一致。在侧孢短芽孢杆菌S2-31的拮抗下抑制了叶枯病菌的生长,其转录组特征也发生显著变化,差异基因主要涉及代谢、细胞过程以及遗传信息处理等途径的相关通路。     

转录组和代谢组分析瘤菌根菌对铁皮石斛的促生机制

为筛选出促进铁皮石斛(Dendrobium officinale)生长的差异表达基因和差异代谢物,对瘤菌根菌与无菌盆栽铁皮石斛苗共生后形成的侧根根系进行转录组、代谢组和双组学联合分析。结果表明,转录组分析共找到262条差异表达基因富集到了35条通路中,其中内质网蛋白质加工通路途径的差异基因最多,其次为氨基糖和核苷酸糖代谢通路。代谢组分析共检测出194个差异代谢物富集到33个KEGG通路中,其中代谢途径的差异代谢物最多有133个,其次为不同环境的微生物代谢途径的差异代谢物有70个。通过联合分析,有9个差异基因的差异表达导致丝氨酸、谷氨酸、D-甘露糖和激素等代谢物的积累量发生变化,这可能是瘤菌根菌促进铁皮石斛生长的重要原因。因此,推测瘤菌根菌促进铁皮石斛生长与氨基酸、糖、植物激素的积累及相关基因的表达变化有关。     

东乡野生稻苗期响应低温胁迫的转录组分析

为了解东乡野生稻（Oryza rufipogon）对低温胁迫的响应机制,对苗期的RNA-seq转录表达谱进行了研究。结果表明,与对照相比,共检测到10 200个差异表达基因（DEGs）,其中5 201个上调表达,4 999个下调表达,其中有426个DEGs位于已报道的水稻耐冷QTL区间,且37个为耐冷调控相关的家族基因。GO功能分类和KEGG代谢路径分析表明,核酸结合转录因子活性、氨基酸生物合成以及光合作用代谢等均参与响应低温胁迫过程。实时荧光定量分析表明,ABA响应蛋白基因、MYB转录因子和40S核糖体蛋白SA基因等12个可能与低温胁迫响应相关的DEGs表达模式与RNA-seq的一致。可见,植物激素传导途径和转录因子相关调控基因在东乡野生稻苗期响应低温胁迫过程中起重要作用。     

基于转录组的八角挥发油合成相关基因挖掘与分析

为更好地挖掘八角(Illicium verum)挥发油合成相关基因，该文对挥发油性状差异显著的优良无性系桂角69号及普通品种砧01号叶片进行了转录组测序及组装注释，并对差异表达基因进行了GO分类和KEGG通路分析。结果表明：(1)转录本经组装后获得84 182条序列，使用NR、NT、Swiss-Prot、KEGG、KOG、GO和Pfam数据库进行序列比对，共注释了59 161条序列，筛选出30 572个差异表达基因。与砧01号相比，桂角69号叶片中上调基因有15 025个，下调基因有15 547个。(2)GO分类结果显示共有20 287个差异基因被注释。KEGG分析结果表明，有21 600个差异基因被注释到133条KEGG通路上，其中挥发油合成相关的单萜生物合成通路、萜类骨架生物合成通路、苯丙素合成通路中的芳樟醇合酶、月桂烯合酶、香叶基香叶基焦磷酸合酶、肉桂酰辅酶A还原酶、咖啡酸3-O-甲基转移酶、肉桂醇脱氢酶等关键酶基因呈差异表达。(3)转录因子分析发现差异表达基因分布于31个转录因子家族，其中MYB家族序列数量最多。该文利用转录组测序技术分析八角优良无性系与普通品种叶片的差异基因及...     

冰菜盐胁迫下的转录组分析

为了解冰菜(Mesembryanthemum crystallinum)叶片抗盐相关基因组学,利用Illumina Hi-seq TM2500高通量测序技术研究冰菜叶片在400 mmol L~(–1) NaCl胁迫下转录组基因的差异表达。结果表明,从400 mmol L~(–1) NaCl胁迫和对照的冰菜叶片中共获得13.01 Gb Clean data,Q30碱基均大于90.08%。共获得123个差异表达基因(DEGs),包括73个上调基因,50个下调基因,其中功能注释的基因有96个。根据Unigene库序列进行GO、COG和KEGG注释,筛选出8个与抗盐性相关差异表达基因,植物激素代谢相关基因,脱落酸8'-羟基化酶、吲哚-3-乙酰酸酰胺合成酶和茉莉酮酸酯ZIM结构域蛋白基因均下调表达,生长素响应蛋白、细胞分裂素合酶基因则上调表达,糖代谢相关基因棉子糖合成酶基因上调表达,质膜H+-ATPase基因上调表达,脱水蛋白基因下调表达。这为冰菜耐盐基因组学和分子生物学的研究奠定基础。     

Transcriptome analysis of the response of silkworm to drastic changes in ambient temperature

Bombyx mori is a poikilothermic insect and is economically important for silk production. Drastic changes in the ambient temperature have a negative impact on sericulture. However, the reason as to why high temperature is associated with the occurrence of diseases in silkworm and the response of silkworm to low temperature remain unclear and were the focus of the present study. Dazao silkworm exposed to 13 °C (DZ-13), 25 °C (DZ-25), and 37 °C (DZ-37) were used for RNA-seq analysis. There were 478 and 194 upregulated differentially expressed genes (DEGs) in DZ-13 and DZ-37 while 49 and 273 downregulated DEGs in DZ-13 and DZ-37, respectively. Eight DEGs were co-upregulated, in which seven genes were for heat shock proteins (Hsps), implying that Hsps play important roles in the tolerance of silkworm to high and low temperature. Gene ontology analysis revealed that the developmental process was downregulated in DZ-13. All the DEGs in the oxidative phosphorylation and insulin signaling pathways were upregulated in DZ-13. Several cuticular proteins and ATP synthesis-related genes were upregulated in DZ-13, suggesting that thickening of the cuticle and increase in the ATPase expression would help silkworms to protect themselves from low temperature-induced stress. Several immune-related genes, such as BmRel and BmSerpin-2, were downregulated in DZ-37, revealing that the resistance of silkworm is decreased under high temperature shock resulting in susceptibility to pathogens. Thus, the increase in the thermo-tolerance of silkworm should be related to the enhancement in the pathogen resistance.

     

刺芹侧耳不同发育时期的转录组差异分析

为了探讨刺芹侧耳子实体生长发育时期的基因表达变化,本文利用高通量测序技术对刺芹侧耳不同发育时期（菌丝期、原基期、子实体时期）进行RNA-Seq分析,在转录水平上解析差异表达基因在刺芹侧耳生长发育过程中的作用和功能。KEGG功能富集显示,菌丝期差异表达基因主要富集在碳代谢和氨基酸代谢中,其中三羧酸循环中编码柠檬酸合酶、乌头酸水合酶、异柠檬酸脱氢酶、琥珀酰辅酶A合成酶、琥珀酸脱氢酶、苹果酸脱氢酶的基因表达量均上调,说明碳代谢和氨基酸代谢是菌丝时期的主要能量来源;原基期上调的差异表达基因主要富集在脂肪酸代谢,其中RT-PCR定量结果显示原基期编码脂肪酸合酶的基因和编码脂酰辅酶A合成酶的基因下调,编码超氧化物酶的基因和编码过氧化氢酶的基因上调,表明脂肪酸代谢和抗氧化酶对刺芹侧耳原基期维持机体的稳定和生物应激方面起着重要作用。子实体时期上调的差异表达基因主要富集在剪接体、类固醇的生物合成以及AMPK信号通路中,说明环境因子对子实体时期有一定的影响。     

Effect of ELOVL6 on the lipid metabolism of bovine adipocytes

This study investigated the effect of ELOVL6 (elongation of very long chain fatty acids protein 6) and its underlying mechanism on lipid metabolism in bovine adipocytes. The ELOVL6 gene was overexpressed in bovine adipocytes by adenoviruses, and RNA sequencing was performed. Overexpression of ELOVL6 showed reduced proportions of C14:0 (Myristic) and C16:0 (palmitate) fatty acids and increased proportions of C18.0 (stearate) and C20:4n6 (arachidonic) fatty acids in adipocytes. In addition, a total of 2170 differentially expressed genes (DEGs) were found, containing 1802 up-regulated and 368 down-regulated genes. KEGG pathway analysis revealed that the down-regulated genes were linked with the regulation of lipolysis and the Wnt signaling pathway. The up-regulated genes were mainly involved in the FoxO signaling pathway; the PI3K-Akt signaling pathway; and the cAMP signaling pathway. In conclusion, our results suggest that ELOVL6 could affect the fatty acid composition in bovine adipocytes. We identified numerous related DEGs and pathways, which may provide a basis for studying the function and molecular mechanism of the ELOVL6 gene in regulating lipid metabolism.     

The genome of <Emphasis Type="Italic">Bacillus aryabhattai</Emphasis> T61 reveals its adaptation to Tibetan Plateau environment

Tibetan Plateau is called ‘the Roof of the World’. Organisms survive there have to adapt to the high altitude environment. By shotgun method, we sequenced the genome of Bacillus aryabhattai T61, which inhabits in the soil at the altitude of 4123 m in Shigatse, Tibetan. Further, we explored the genomic basis for its adaptations to the plateau environment. The results showed that B. aryabhattai T61 has evolved an array of ROS defense systems and sporulation system for adaptations to the stresses caused by the plateau strong ultraviolet radiation, extreme oxygen limitation and low temperature. Specifically, B. aryabhattai T61 encodes the ResE–ResD two-component to sense the oxygen limitation and regulates COX15 for aerobic and anaerobic respiration. The two-component system DesK–DesR, which regulates the gene Des initiating the biosynthesis of unsaturated fatty acids, along with 33 temperature-shock proteins contribute to low temperature adaptation. With the comparative analysis, we deduced the novel gene cbiY may be involved in cobalamin biosynthesis. We also found that B. aryabhattai T61 may have novel regulatory mechanisms for sporulation initiation. B. aryabhattai T61 is the first Tibetan strain with high quality genome sequenced. The genome provides a paradigm for understanding the adaptations to the plateau environment in Bacteria kingdom.     

Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana

Early seedling emergence can increase plant fitness under competition. Seed oil composition (the types and relative amounts of fatty acids in the oils) may play an important role in determining emergence timing and early growth rate in oilseeds. Saturated fatty acids provide more energy per carbon atom than unsaturated fatty acids but have substantially higher melting points (when chain length is held constant). This characteristic forms the basis of an adaptive hypothesis that lower melting point seeds (lower proportion of saturated fatty acids) should be favored under colder germination temperatures due to earlier germination and faster growth before photosynthesis, while at warmer germination temperatures, seeds with a higher amount of energy (higher proportion of saturated fatty acids) should be favored. To assess the effects of seed oil melting point on timing of seedling emergence and fitness, high‐ and low‐melting point lines from a recombinant inbred cross of Arabidopsis thaliana were competed in a fully factorial experiment at warm and cold temperatures with two different density treatments. Emergence timing between these lines was not significantly different at either temperature, which aligned with warm temperature predictions, but not cold temperature predictions. Under all conditions, plants competing against high‐melting point lines had lower fitness relative to those against low‐melting point lines, which matched expectations for undifferentiated emergence times.     

萱草叶片响应低温胁迫的转录组分析

低温胁迫是萱草（Hemerocallis fulva）生长过程中经常会遭遇的一种非生物胁迫。比较了萱草叶片在低温处理（10、5、0 ℃）下转录组与对照（15 ℃）数据的差异,共筛选出差异表达基因2 457个,其中上调基因1 253个,下调基因1 204个。差异表达基因主要富集在细胞过程、代谢过程和催化活性等49个GO过程,代谢途径、次生代谢产物的生物合成、植物激素信号转导等42条KEGG代谢途径中。其中参与植物激素信号转导通路的差异表达基因发生了不同程度的变化,GH3.10基因上调至对照组的13.624倍,IAA1基因下调0.120倍;参与可溶性糖合成通路的差异基因发生了0.076~28.114倍不同程度的变化。随后对3个低温处理组共有的29个差异表达基因进行热图和网络调控分析,基于基因在网络调控中的位置,对ABCF5、OFPs和SWEETs等基因在冷应答的作用进行了分析。本研究结果为进一步挖掘萱草低温响应的关键基因及耐寒萱草种质开发、分子育种提供了一定的理论支撑。     

Temperature independence of the composition of triglyceride fatty acids synthesized de novo by the mosquito

The hypothesis that depot fat is more unsaturated when it is synthesized at lower temperatures was tested in the mosquito. Female mosquitoes (Aedes sollicitans) were starved until no triglycerides remained. A single dose of sugar was fed and the mosquitoes were maintained at different temperatures. Approximately the same amount of triglyceride was synthesized per mosquito at each temperature, although at different rates. Mosquitoes maintained at low temperatures did not synthesize more unsaturated triglycerides than those at higher temperatures: the fatty acid composition was essentially the same from 10 to 35 degrees. The triglycerides synthesized from sugar contained no poly-unsaturated fatty acids. Total amounts and composition of phospholipid fatty acids remained unaltered during sugar feeding. When deprived of food, the mosquitoes catabolized triglyceride fatty acids randomly; cold-exposure did not cause selective retention or utilization of any individual fatty acid.     

Haemolymph amino acid and sugar levels in locusts fed nutritionally unbalanced diets

Aspects of pre- and post-ingestive compensation were investigated in locusts (Locusta migratoria) fed nutritionally unbalanced artificial diets containing 7% protein and 21% digestible carbohydrate (7:21) or 21% protein and 7% digestible carbohydrate (21:7). Feeding behaviour and haemolymph levels of amino acids and sugars were measured in locusts fed ad libitum on these diets. Locusts fed the high-protein diet had chronically elevated haemolymph levels of 15 out of 19 amino acids measured compared to locusts fed the low protein diet. However, haemolymph levels of lysine, alanine, aspartic acid and glutamic acid did not differ between diets, suggesting some specific regulatory mechanism for these amino acids. Haemolymph glucose and trehalose reflected levels of carbohydrate in the diets, being high in insects fed diet 7:21 relative to those given diet 21:7. These data are discussed in relation to the physiological and behavioural bases of nutritional homeostasis.Abbreviations AA amino acid(s) - PRO protein - CHO carbohydrate - PBS phosphate-buffered saline - MW molecular weight     

基于RNA-Seq的向日葵脂肪酸合成基因筛选与分析

向日葵(Helianthus annuus L.)是世界四大油料作物之一。为解析向日葵主要脂肪酸组分的生物合成分子机制,选用高油酸自交系J9、低油酸自交系P50为研究材料;采用错期播种同期采样试验,以液相色谱测定授粉后不同样品籽粒的脂肪酸组分与含量;利用RNA-Seq技术,对不同样品测序,获得各样品与脂肪酸合成相关的基因表达数据,以气象学数据、液相色谱数据、向日葵基因组数据和转录组数据为基础,采用生物信息学方法分析相关数据。结果表明：(1)高油酸向日葵材料脂肪酸组分和含量受温度影响小,而低油酸材料易受温度影响;(2)J9和P50的12个样本的高表达基因数在7500个左右,而中、低表达基因数相当,是高表达基因的两倍,约15000个;(3)品种特异性表达基因和品种间特异表达基因去除重复后,在J9和P50在-CK和S数据集得到15885个,GO功能富集获得的与脂质代谢直接相关的403个DEGs 映射到与的脂质代谢相关的KEGG代谢通路,累计29个DEGs直接参与了19条相关KEGG通路。本研究将为深入解析向日葵脂肪酸代谢分子机制提供新信息。     

Identification of novel protein targets regulated by maternal dietary fatty acid composition in neonatal rat liver

Polyunsaturated fatty acids regulate metabolic pathways, which in early development could have important consequences to adaptation to extra-uterine life and programming of metabolic pathways. Female rats were fed one of two diets identical in all nutrients, except that the fat in one diet was high in unsaturated fatty acids (UFA) and the other low UFA, through gestation and lactation. Two-dimensional sodium dodecylsulfate polyacrylamide gel electrophoresis of protein extracts from 3-day old pup liver resolved over 800 proteins. Employing MALDI-TOF MS and peptide mapping we identified 11 proteins that differed more than three-fold between the groups, 10 up regulated and one down regulated in the high UFA group. The up-regulated proteins included fructose-1,6-bisphosphatase 1, glycerol-3-phosphate dehydrogenase, galactokinase 1, 40S ribosomal protein SA, elongation factor 1-gamma, protein disulfide-isomerase A6, catalase, cytokeratin-8 and 60 kDa heat shock protein, and the down-regulated protein was argininosuccinate synthase, none having been previously reported to be regulated by fatty acids in the developing liver. We further determined that fructose-1,6-biphosphatase is acetylated at the N-terminus. We demonstrate that early fatty acid nutrition impacts hepatic metabolic pathways relevant to gluconeogenesis, redox balance and nitric oxide signaling.