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1.
Newly emerging or re‐emerging diseases are a constant and significant threat to agricultural production, so prompt and accurate identification of the causative agents is required for rapid and appropriate disease management. Classical methods of pathogen detection can be successfully supplemented by next‐generation sequencing (NGS), whereby sequence analysis can help in the discovery of new or emerging diseases. In 2007, hop growers in Slovenia reported the appearance of severely stunted hop plants, a phenomenon that spread rapidly within hop gardens and among farms. Classical diagnostic methods were unable to detect a new pathogen; therefore, single step high‐throughput parallel sequencing of total RNA and small RNAs from plants with and without symptoms was employed to identify a novel pathogen. The sequences were assembled de novo and also mapped to reference genomes, resulting in identification of a novel sequence of Citrus bark cracking viroid (CBCVd) in the stunted hop plants. Furthermore, the presence of this novel pathogen on hop was confirmed by RT‐PCR analysis of 59 plants with symptoms from 15 hop gardens, representing the main outbreak locations identified by systematic disease monitoring, and small RNA Illumina sequencing of the bulked RNA sample. The high infectivity of the newly identified CBCVd was also confirmed by biolistic inoculation of two hop cultivars, which developed aggressive symptoms in controlled conditions. This study shows the feasibility of deep sequencing for the identification of causative agents of new diseases in hop and other plants. 相似文献
2.
为进一步探明美洲水貂酪氨酸酶(TYR)基因的结构和功能信息,对美洲水貂TYR基因编码蛋白进行生物信息学分析,同时构建TYR基因的系统发育树。结果表明:美洲水貂TYR基因共编码531个氨基酸,其编码产物为不稳定的亲水蛋白;二级结构主要以α-螺旋和无规卷曲为主,含有1个酪氨酸酶超家族结构域,存在信号肽、跨膜结构域和二硫键;该蛋白主要在内质网中发挥细胞被膜、运输和结合的作用,同时还通过信号转导在细胞内发挥其生物学作用;系统进化情况和动物分类学基本一致,美洲水貂TYR基因与雪貂、家犬的亲缘关系最近。美洲水貂TYR基因编码蛋白在生物进化中具有较强保守性,该基因结构和功能的分析为水貂TYR基因遗传特性的进一步研究奠定了基础。 相似文献
3.
随着拟南芥和水稻基因组测序的完成,对植物基因组学的研究转入到了蛋白质组学的研究。笔者重点介绍了蛋白质组学的概念和关键技术。蛋白质组学的关键技术包括双向电泳技术、高效液相色谱技术、质谱技术、蛋白质组学的相关数据库等。 相似文献
4.
植物
5.
XU Yong-qiang WANG Jin-jun JIANG Hong-bo DOU Wei TANG Pei-an AN Feng-ming 《中国农业科学(英文版)》2009,8(10):1210-1218
An allele of CYP6BQI3, named CYP6BQ 13v2 (GenBank accession no. FJ209361), was isolated from the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) by RT-PCR. The cDNA sequence of CYP6BQ13v2, 1 563 bp in length, contains an open reading frame of 1 554 nucleotides encoding a putative protein of 518 amino acid residues with a predicted molecular weight of 59.92 kDa and a theoretical pl of 7.60. The putative protein contains the classic hemebinding sequence motif F××G×××C×G (residues 456-465) conserved among all P450 enzymes as well as other characteristic motifs of all cytochrome P450s. It shares 98% identity with the previously published sequence of CYP6BQ13 (GenBank accession no. XP967146) from the T. castaneum genome project. Phylogenetic analysis of amino acid sequences from members of various P450 families indicated that there was closer phylogenetic relationship of CYP6BQ 13v2 with CYP302A1 and CYP307A1 mediating synthesis of the insect molting hormone, distant relationship with CYP6B1 metabolizing plant allelochemicals, CYP6D 1 linking to pyrethroid resistance and other members of CYP6 family. Expression test of the gene in the adults and immature stages of T. castaneum by quantitative real-time PCR revealed that CYP6BQ13v2 is expressed in all life stages investigated. The mRNA expression level in 1st instar larvae was 14.9- and 3.86-fold higher than those in pupae and adults, respectively. The CYP6BQ13v2 expression levels appeared in the order of 1st instar larvae, followed by 4th instar larvae, 7th instar larvae, adult, and pupae from high to low. The more bioinformation of CYP6BQ 13v2 was also analyzed. 相似文献
6.
HUANG Huan-huan ZHANG Zhong-hua ZHANG Zheng-hai MAO Sheng-li WANG Li-hao ZHANG Bao-xi 《农业科学学报》2025,10(10)
SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pl’ software, while 116915 EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 microsatellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tri-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers. Abstract SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pl’ software, while 116915 EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 microsatellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tri-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers.
7.
张宇;宋彦婷;郭丽娜;郭媛 《南方农业学报》2025,56(1):287-294
【目的】探究意大利蜜蜂(Apis mellifera)化学感受蛋白CSP2(AmelCSP2)序列特征及AmelCSP2基因组织表达特性,为阐明AmelCSP2蛋白的生物学功能提供理论参考。【方法】利用ProtParam、ProtScal、SignalP-5.0、TMHMM-2.0、PSORTb 3.0.3、DictyOGlyc-1.1、NetNGlyc-1.0、NetPhos 3.1、SWISS-MODEL、CD-search、SMART和STRING等生物信息学软件预测AmelCSP2蛋白理化性质、亲/疏水性、信号肽、跨膜结构域、亚细胞定位、O-糖基化位点、N-糖基化位点、磷酸化位点、高级结构、模体、结构域和蛋白互作网络。采用实时荧光定量PCR检测AmelCSP2基因在意大利蜜蜂触角、头(不含触角)、胸、腹、足、翅中的相对表达量。【结果】AmelCSP2蛋白编码117个氨基酸残基,理论分子量约13.06 kD,理论等电点(pI)为9.27,分子脂肪系数为92.56,不稳定系数为59.68,平均亲水性指数为-0.254,为两性不稳定蛋白。AmelCSP2蛋白在第1~21位氨基酸残基处有信号肽,不含跨膜结构域,主要定位于细胞周质、细胞质和细胞外膜。AmelCSP2蛋白不存在糖基化位点,但存在20个磷酸化位点。AmelCSP2蛋白二级结构中无规则卷曲占42.74%,α-螺旋占38.46%,延伸链占18.80%,蛋白三级结构较稳定。AmelCSP2蛋白属于OS-D超家族,在第32~116位氨基酸残基处存在唯一蛋白结构域OS-D。AmelCSP2蛋白可能与PYX2、ASP3、OBP3c、NT-7及OBP14蛋白存在相互作用。AmelCSP2基因在意大利蜜蜂的触角、头(不含触角)、胸、腹、足、翅中均有表达,触角中AmelCSP2基因相对表达量显著高于其他组织(P<0.05)。【结论】AmelCSP2蛋白具有典型的OS-D超家族结构域,并含有多个磷酸化位点,可能通过磷酸化修饰调控其功能。AmelCSP2蛋白可能与PYX2、ASP3、OBP3c、NT-7及OBP14蛋白相互作用,参与化学感受信号传导。AmelCSP2基因在意大利蜜蜂触角中高表达,其可能在嗅觉感受系统中承担气味分子运输功能。 相似文献
8.
林世锋;王仁刚;杨志晓;王自力;李莉;朱秀;陈越男 《南方农业学报》2025,56(3):816-826
【目的】克隆豆伞滑刃线虫(Bursaphelenchus doui)类转甲状腺素(Transthyretin-like,TTL)基因Bd-TTL-1并进行表达特性分析,为进一步研究该基因的生物学功能打下基础。【方法】以植物寄生线虫豆伞滑刃线虫为试验材料,以其体前端cDNA为试验方,体后端cDNA为驱动方,利用固相消减杂交方法构建豆伞滑刃线虫体前端特异cDNA文库。利用反向Northern杂交和测序筛选文库,结合RACE技术获得Bd-TTL-1基因全长序列,并利用生物信息学软件及数据库对Bd-TTL-1蛋白的理化性质、信号肽、跨膜区、同源性和保守结构域进行预测分析。利用实时荧光定量PCR和原位杂交分别进行基因发育模式和表达定位分析。【结果】成功构建1个豆伞滑刃线虫体前端特异cDNA文库。通过反向Northern杂交、测序与RACE技术相结合的方法克隆获得豆伞滑刃线虫TTL全长基因Bd-TTL-1,GenBank登录号PQ276066。Bd-TTL-1基因DNA编码区全长497 bp,包括2个外显子和1个内含子;cDNA编码区全长435 bp,编码144个氨基酸。预测Bd-TTL-1蛋白的相对分子量为15.86 kD,理论等电点为9.37;Bd-TTL-1蛋白含有1个典型且保守的TTL蛋白结构域,存在信号肽但无跨膜结构域,属于分泌性蛋白。实时荧光定量PCR结果显示,Bd-TTL-1基因在豆伞滑刃线虫各发育阶段均有表达,但在虫卵期表达微弱,显著低于其他发育阶段(P<0.05)。原位杂交结果显示,Bd-TTL-1基因在豆伞滑刃线虫的食道腺特异表达。【结论】豆伞滑刃线虫Bd-TTL-1蛋白的氨基酸序列含有1个TTL蛋白保守结构域,是一种具有信号肽但无跨膜结构域的分泌性蛋白;Bd-TTL-1基因在豆伞滑刃线虫食道腺中特异表达,初步推测编码蛋白在寄生过程中通过口针释放到体外发挥作用。 相似文献
9.
通过应用生物信息学分析的方法,以已知的丝状真菌Lae A基因序列为模板,对丝状真菌中的全局性调控因子Lae A进行结构与功能预测,旨在揭示其在丝状真菌次级代谢过[1]程中的作用提供科学依据。结果表明:丝状真菌全局性调控因子Lae A是亲水蛋白,无跨膜区且无信号肽;在氨基酸序列第250-275位之间可能存在卷曲结构;二级结构中,α-螺旋所占比例为29.84%、β-折叠占15.59%、β-转角占4.30%,无规则卷曲占50.27%;在第138-226位之间有一个结构域——Methyltransf_25 domain;预测结果显示该蛋白氨基酸序列不能够得到较为理想的蛋白质三维结构图;Lae A蛋白具有翻译途径tRNA甲基化酶以及Ⅰ类SAM依赖性甲基转移酶的作用。 相似文献
10.
旨在探讨中国荷斯坦奶牛的特异性蛋白1(specificity protein,SP1)基因结构特征及其对奶牛乳脂合成的影响。根据NCBI已经公布的奶牛SP1基因序列(NM_001078027.1),利用生物信息学分析其序列保守性、理化性质、蛋白亲水性、蛋白质结构及互作蛋白;采用PCR技术扩增并克隆SP1基因CDS序列。然后,选取6头健康的中国荷斯坦奶牛,分别取泌乳期和干奶期奶牛乳腺组织,运用实时荧光定量PCR和Western blot方法检测SP1基因在不同时期奶牛乳腺组织中的表达情况。分离并纯化泌乳期奶牛乳腺上皮细胞,通过SP1过表达及干扰检测其对乳脂合成的影响,分别进行3次独立试验。结果显示,SP1基因序列在不同物种间高度保守,与山羊相似度最高(98.94%)。奶牛SP1基因CDS区序列长2 361 bp,编码786个氨基酸,蛋白分子质量为80 902.17 u,理论等电点为6.94。平均疏水指数为-0.438,为不稳定的亲水性蛋白。SP1序列包含3个锌指结构,SP1蛋白二级结构以无规则卷曲(52.29%)为主。STRING蛋白互作分析结果显示,SP1与转录因子AP-1(JUN)、雌激素受体α(ERα)、MYC原癌基因蛋白(MYC)、TATA盒结合蛋白(TBP)等蛋白存在相互作用。实时荧光定量PCR和Western blot结果显示,SP1的mRNA和蛋白在泌乳期的表达量显著高于干奶期(P<0.01)。在奶牛乳腺上皮细胞中过表达SP1显著增加细胞甘油三酯的合成(P<0.01),而干扰SP1的表达,甘油三酯合成显著降低(P<0.01)。以上结果提示,SP1正向调控乳脂合成,分析SP1基因结构和功能为深入研究SP1对泌乳奶牛乳脂合成调控机制提供理论依据。 相似文献