为探究广丰千金薯和铁棍山药在分子水平的差异,以广丰千金薯(QJS)和铁棍山药(TGSY)试管苗的微型块茎为试验材料进行转录组分析。结果表明:QJS组和TGSY组样本间相关系数为0.42。QJS组和TGSY组表达量FPKM的对数值在0~1.5,表达量密度在0~1.0。与TGSY组相比,QJS组有4 765个基因下调,有5 112个基因上调。QJS组和TGSY组表达的共有基因有25 207个,QJS组单独表达的基因有5 261个,TGSY组单独表达的基因有3 571个。QJS组和TGSY组共发现611 498个单核苷酸多态性(single nucleotide polymorphism,SNP)位点和12 056个简单重复序列(simple sequence repeats,SSR)。与TGSY组相比,QJS组的淀粉合成酶3、α-淀粉酶3、β-淀粉酶、类黄酮3'-单加氧酶、类黄酮3'-羟化酶、花青素合酶等基因上调,而颗粒结合淀粉合酶2、蔗糖合酶1、扩展蛋白2和苯丙氨酸解氨酶等基因下调。这可能是广丰千金薯微型块茎肉质绵密粉嫩、软糯爽口、胁迫防御、食后易胀的内在原因。结果可以为广丰千金薯的品种鉴定和分子育种提供参考。

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

Sugars have a central regulatory function in steering plant growth. This review focuses on information presented in the past 2 years on key players in sugar-mediated plant growth regulation, with emphasis on trehalose 6-phosphate, target of rapamycin kinase, and Snf1-related kinase 1 regulatory systems. The regulation of protein synthesis by sugars is fundamental to plant growth control, and recent advances in our understanding of the regulation of translation by sugars will be discussed.

根系是植物生长发育必不可缺的器官，不仅起到固定、支持植物的作用，还能从土壤中吸收植物生长发育必需的水分和无机盐。在植物根系生命活动中糖充当着营养成分和信号分子的双重作用，且与植物激素作用影响根系生长发育。近年来，国内外学者对糖调控植物根系生长发育做了大量研究，笔者综述了糖对根系生长发育的影响，介绍了糖信号转导及糖信号转导调控根系生长发育的机理，并从糖与植物激素的共同作用方面总结了糖调控根系生长发育机理的研究进展，以期为后续糖调控植物根系的相关研究提供参考。

Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log fold change (FC) and down-regulation with ≤ -2 log FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.

【目的】土壤盐渍化是制约作物生产的重要非生物胁迫因子之一,高粱耐盐性强,进行高粱耐盐基因挖掘及分子机制研究是开发和利用盐渍土壤的有效途径,通过转录组测序分析与高粱耐盐相关的基因调控机制和代谢通路,挖掘高粱耐盐潜力。【方法】 通过以筛选出的极耐盐品种八叶齐和盐极敏感品种PL212为试验材料,采用盆栽沙培,在播种后20 d（5叶期）采用180 mmol·L ^-1的 NaCl 溶液漫灌模拟盐逆境,盐胁迫48 h后取幼叶,并连同对照（未经过盐处理）的同期幼苗共4个样品提取RNA,进行转录组测序,采用qRT-PCR方法对测序结果进行验证。 【结果】 耐盐和盐敏感材料分别在盐渍和非盐渍处理下的4个样品间共检测到1 338个差异表达基因,包括819个上调基因和519个下调基因。聚类分析发现在应答盐渍胁迫逆境时,5个依赖性氧合酶超家族蛋白、4个富含半胱氨酸的激酶、3个谷胱甘肽S-转移酶和3个重金属运输/解毒超家族蛋白相关基因表现出明显的上调表达和下调表达,还发现1个K ⁺转运蛋白基因在耐盐调节中起着重要作用。GO分析发现在15 418个基因中获得4 528个有效GO注释条目,同时耐盐和盐敏感材料在遭受盐逆境时的生物过程、细胞组分和分子功能3个方面均存在较大差异。生物过程中代谢过程、细胞过程耐盐材料明显高于盐敏感材料,耐盐材料的生理过程中较盐敏感材料增加了多生物过程和定位这两个过程,很可能与耐盐材料盐抗性较强密切相关。差异基因KEGG分析结果显示耐盐和盐敏感材料在对照和盐渍胁迫条件下的苯丙烷类生物合成、苯丙氨酸代谢、类黄酮生物合成3个途径中差异基因表达较多,可能是造成耐盐和盐敏感材料耐盐性差异较大的重要原因。 【结论】 高粱耐盐调控基因表达涉及生物过程、细胞组分和分子功能多个方面,生物过程和定位这两个过程是提高高粱耐盐性的关键;苯丙烷类生物合成、苯丙氨酸代谢、类黄酮生物合成3个途径的基因表达很可能是造成盐害的重要原因。

苦瓜在生长季节遇到低温会影响其生长发育和产量,限制了种植分布区域。为了研究苦瓜耐寒性的分子机制,本研究以苦瓜自交系43为试验材料,在8℃低温胁迫处理后观察其表型并测定相关生理生化指标,再利用转录组测序技术从生理角度结合分子水平对苦瓜低温胁迫机制进行生物信息学分析。结果表明,在8℃低温胁迫下,苦瓜表现出耐低温适应性,在低温胁迫下丙二醛(MDA)含量、脯氨酸含量及电解质渗透率均呈现显著变化。分析了低温胁迫0和12 h后的转录组变化,结果发现低温胁迫处理后有916个基因上调,369个基因下调。对差异表达基因进行通路注释分析,发现大量与低温胁迫相关的代谢途径。进一步筛选到10个在其他物种报道过可能与冷胁迫相关的基因,包括MYB、WRKY以及NAC转录因子等。对植物耐低温相关的候选基因进行了实时荧光定量PCR(qRT-PCR)表达谱分析,结果与生理表型变化相吻合,同时进一步证实了RNA-seq数据的准确性。本研究基于全基因组水平分析苦瓜在低温胁迫下的转录组变化,以及耐低温相关基因动态变化和生理反应的分子机制,为揭示苦瓜中的耐寒性机理和筛选遗传改良候选基因提供了一定基础。

研究比较了枇杷（Eriobotrya japonica Lindl.）不同发育阶段花果的低温响应机制。以花蕾、完全开放的花和花后2周左右的幼果为试验材料,-3 ℃低温处理12 h,以未经低温处理样品为对照,测定生理生化指标并进行转录组测序分析。低温胁迫导致细胞膜破坏,超氧阴离子产生速率、丙二醛和脯氨酸含量、抗氧化酶活性明显升高。总体上抗低温能力为花蕾 > 花 > 幼果。转录组测序分析共获得6 987个差异表达基因（DEG）,对这些基因进行通路注释分析,发现大量与低温胁迫相关的代谢途径,其中碳水化合物代谢中的糖酵解/糖异生、乙醛酸和二羧酸代谢及磷酸肌醇代谢途径,氨基酸代谢中的色氨酸代谢和酪氨酸代谢途径,酯类代谢中的甘油磷脂代谢、α-亚麻酸代谢和甘油酯代谢途径,次生代谢中的异喹啉生物碱生物合成途径以及能量代谢中的硫代谢途径在3个花果发育时期低温与对照的比较组中显著富集,说明这几个途径都是枇杷花果响应低温胁迫的重要代谢途径。“苯丙烷类生物合成”途径在前两个时期比较组中富集水平较高,氨基酸代谢相关途径在幼果比较组中富集更多。另外,从低温处理相关差异表达基因中筛选到了53个AP2-EREBP基因,14个WRKY基因和15个NAC基因,并对其中12个低温响应相关转录因子基因进行了qRT-PCR表达分析,进一步证实了转录组数据的准确性。