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学者姓名：张慧
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Abstract ：
The accessory proteins Hyponastic-like 1 (HYL1) and Serrated (SE) enhance the precise and efficient processing of miRNAs by Dicer-like 1 (DCL1), which is important for proper miRNA function. However, other factors determining the precision and efficiency of miRNA biogenesis are not well-known. Here, we found that an asymmetric bulge (AB) at the 3 ' end of miR-5p (produced from the 5 ' arm of the pre-miRNA) reduced the precision of the second cleavage, whereas an AB at other sites of miR-5p mainly affected the accumulation level of miR-5p in transient expression in Nicotiana benthamiana. In contrast, many ABs in miR-3p (produced from the 3 ' arm of the pre-miRNA) impose strong negative impact on the processing precision and the accumulation level of miR-5p in N. benthamiana. Arabidopsis DCL1/SE/HYL1 complex-mediated miRNA processing was reconstituted in Saccharomyces cerevisiae to further investigate AB-mediated interference with DCL1 processing. With this system, the positional effect of AB on miRNA processing was tested. The results showed that ABs on the middle of miR-5p have less of an impact on DCL1 cleavage efficiency and precision, whereas those on miR-3p or near the ends of miR-5p strongly reduce DCL1 cleavage activity, precision or both. Studies using the yeast miRNA processing system and transgenic Arabidopsis also revealed the importance of the interaction between the 2-nt 3 ' overhang of pre-miRNA and the 3 ' overhang binding pocket (3 ' BP) on the precision of the second cleavage reaction for many endogenous miRNAs. These findings provide new insights into the mechanism of miRNA biogenesis.
Keyword ：
asymmetric bulge asymmetric bulge biogenesis biogenesis Dicer-like 1 Dicer-like 1 miRNA miRNA PAZ domain PAZ domain precision precision
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| GB/T 7714 | Zhang, Hui , Li, Feng . Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing [J]. | PLANT JOURNAL , 2024 , 120 (1) : 109-122 . |
| MLA | Zhang, Hui 等. "Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing" . | PLANT JOURNAL 120 . 1 (2024) : 109-122 . |
| APA | Zhang, Hui , Li, Feng . Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing . | PLANT JOURNAL , 2024 , 120 (1) , 109-122 . |
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PcHIPPs/PcHPPs是一类细胞内可溶性金属结合蛋白，在调节植物重金属稳态、解毒机制、重金属耐受等方面发挥重要作用，目前关于HIPPs/HPPs基因家族在多花黄精中还未有人研究.基于多花黄精不同转录组数据，采用生物信息学进行理化性质分析、亚细胞定位和保守基序及系统进化树分析，并对其功能进行初步分析，研究HIPPs/HPPs基因在不同铅处理下的表达情况.结果表明：从多花黄精中鉴定出68个PcHIPPs和43个PcHPPs基因；PcHIPPs基因家族的氨基酸数为134-501，分子量介于15.53-53.09 ku之间，等电点介于5.12-9.88;PcHPPs基因的氨基酸数为101-352，分子量介于11.46-38.23 ku，等电点介于5.58-10.41；亚细胞定位预测表明，PcHIPPs/PcHPPs基因有73个分布在细胞核内；通过KEGG分析发现PcHPP3、PcHIPP28-5、PcHIPP28-6、PcHPP1-5参与到代谢过程；PcHIPPs/PcHPPs基因在多花黄精根状茎中主要发挥作用，在盐胁迫处理48 h下大部分PcHIPPs/PcHPPs基因表现出明显的下调现象；多花黄精组培苗在铅处理中叶片萎缩、枯黄逐渐加重，并且低浓度的铅胁迫对植物叶绿素含量具有一定的促进作用，而高浓度的铅胁迫对植物叶绿素含量具有抑制作用；此外，PcHIPPs/PcHPPs基因总体上随着铅浓度的增加呈现出先升高后降低的表达趋势.本研究表明PcHIPPs/PcHPPs基因在多花黄精铅胁迫中起重要调控作用，为PcHIPPs/PcHPPs基因在重金属胁迫响应中的功能奠定基础.（图7表3参43）
Keyword ：
HIPPs基因 HIPPs基因 HPPs基因 HPPs基因 多花黄精 多花黄精 生物信息学分析 生物信息学分析 表达分析 表达分析
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| GB/T 7714 | 李小利 , 朱田圆 , 班景洁 et al. 基于多花黄精转录组的HIPPs/HPPs基因家族鉴定与表达调控 [J]. | 应用与环境生物学报 , 2024 , 30 (01) : 133-143 . |
| MLA | 李小利 et al. "基于多花黄精转录组的HIPPs/HPPs基因家族鉴定与表达调控" . | 应用与环境生物学报 30 . 01 (2024) : 133-143 . |
| APA | 李小利 , 朱田圆 , 班景洁 , 王庆爽 , 陈翠蓉 , 张慧 et al. 基于多花黄精转录组的HIPPs/HPPs基因家族鉴定与表达调控 . | 应用与环境生物学报 , 2024 , 30 (01) , 133-143 . |
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为了探究低磷（P）胁迫下不同亲缘关系邻株对杉木生长的影响规律，验证杉木根系是否具有亲缘识别行为，采用室内盆栽控制试验，选择2个杉木半同胞家系（No.32、No.28）为试验材料，利用
Keyword ：
杉木 杉木 根系亲缘识别 根系亲缘识别
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| GB/T 7714 | 李亚超 , 王讷敏 , 张慧 et al. 基于13C标记的低磷胁迫杉木根系亲缘识别分析 [J]. | 生态学报 , 2024 , 44 (23) : 10827-10837 . |
| MLA | 李亚超 et al. "基于13C标记的低磷胁迫杉木根系亲缘识别分析" . | 生态学报 44 . 23 (2024) : 10827-10837 . |
| APA | 李亚超 , 王讷敏 , 张慧 , 林文奖 , 马祥庆 , 吴鹏飞 . 基于13C标记的低磷胁迫杉木根系亲缘识别分析 . | 生态学报 , 2024 , 44 (23) , 10827-10837 . |
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The origin of sociality represents one of the most important evolutionary transitions. Insect sociality evolved in some hemipteran aphids, which can produce soldiers and normal nymphs with distinct morphology and behaviour through parthenogenesis. The lack of genomic data resources has hindered the investigations into molecular mechanisms underlying their social evolution. Herein, we generated the first chromosomal-level genome of a social hemipteran (Pseudoregma bambucicola) with highly specialized soldiers and performed comparative genomic and transcriptomic analyses to elucidate the molecular signatures and regulatory mechanisms of caste differentiation. P. bambucicola has a larger known aphid genome of 582.2 Mb with an N50 length of 11.24 Mb, and about 99.6% of the assembly was anchored to six chromosomes with a scaffold N50 of 98.27 Mb. A total of 14,027 protein-coding genes were predicted and 37.33% of the assembly were identified as repeat sequences. The social evolution is accompanied by a variety of changes in genome organization, including expansion of gene families related to transcription factors, transposable elements, as well as species-specific expansions of certain sugar transporters and UGPases involved in carbohydrate metabolism. We also characterized large candidate gene sets linked to caste differentiation and found evidence of expression regulation and positive selection acting on energy metabolism and muscle structure, explaining the soldier-specific traits including morphological and behavioural specialization, developmental arrest and infertility. Overall, this study offers new insights into the molecular basis of social aphids and the evolution of insect sociality and also provides valuable data resources for further comparative and functional studies.
Keyword ：
caste differentiation caste differentiation chromosomal genome assembly chromosomal genome assembly gene expression gene expression social aphid social aphid
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| GB/T 7714 | Zhang, Hui , Liu, Qian , Lu, Jianjun et al. Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality [J]. | MOLECULAR ECOLOGY RESOURCES , 2024 . |
| MLA | Zhang, Hui et al. "Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality" . | MOLECULAR ECOLOGY RESOURCES (2024) . |
| APA | Zhang, Hui , Liu, Qian , Lu, Jianjun , Wu, Liying , Cheng, Zhentao , Qiao, Gexia et al. Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality . | MOLECULAR ECOLOGY RESOURCES , 2024 . |
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植物类谷氨酸受体(glutamate receptor-like,GLR)是一类重要的Ca~(2+)通道蛋白，在植物的生长发育以及响应生物和非生物胁迫等方面有着重要作用。本研究基于香蕉基因组数据，对香蕉GLR基因家族进行全基因组鉴定，分析基本理化性质、基因结构、保守基序、启动子顺式作用元件和进化关系，并采用实时荧光定量聚合酶链式反应(real-time fluorescence quantitative polymerase chain reaction, RT-qPCR)验证GLR家族部分成员在4℃低温和不同激素处理下的表达模式。研究结果表明：香蕉A (Musa acuminata)基因组有19个MaGLR家族成员、B (Musa balbisiana)基因组16个MbGLR家族成员、阿宽蕉(Musa itinerans)基因组有14个MiGLR家族成员；大多数成员为稳定蛋白，绝大多数成员具有信号肽，均有3–6个跨膜结构；亚细胞定位预测均定位于质膜上，在染色体上无规则分布。进化树分析发现，香蕉GLR分为3个亚族。启动子顺式作用元件和转录因子结合位点(transcription factor binding site, TFBS)预测结果显示，香蕉GLR存在多种与激素、胁迫相关响应元件以及18种TFBS。RT-qPCR分析表明，MaGLR1.1、MaGLR3.5在4℃低温胁迫下积极响应且脱落酸、茉莉酸甲酯处理中均有显著表达。本研究结果表明GLR是一种高度保守的离子通道家族，在香蕉生长发育过程和抗逆性方面可能发挥着重要作用。
Keyword ：
GLR GLR 低温 低温 家族鉴定 家族鉴定 表达分析 表达分析 香蕉 香蕉
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| GB/T 7714 | 罗彬彬 , 张慧 , 李丹 et al. 香蕉GLR基因家族全基因组鉴定及其响应低温与脱落酸/茉莉酸甲酯的表达分析 [J]. | 生物工程学报 , 2023 , 39 (07) : 2874-2896 . |
| MLA | 罗彬彬 et al. "香蕉GLR基因家族全基因组鉴定及其响应低温与脱落酸/茉莉酸甲酯的表达分析" . | 生物工程学报 39 . 07 (2023) : 2874-2896 . |
| APA | 罗彬彬 , 张慧 , 李丹 , 吴秋桢 , 葛婉君 , 朱田圆 et al. 香蕉GLR基因家族全基因组鉴定及其响应低温与脱落酸/茉莉酸甲酯的表达分析 . | 生物工程学报 , 2023 , 39 (07) , 2874-2896 . |
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【目的】PLT(Plethora)属于AP2/ERF型转录因子，在植物生长发育及抗胁迫等过程中发挥重要作用。本文旨在探究多花黄精PLT(Polygonatum cyrtonema Hua PLT,PcPLT)基因在根状茎器官生长发育中及盐胁迫下的调控作用，为深入研究PcPLT基因的功能提供理论依据。【方法】基于多花黄精转录组数据库进行PcPLT基因家族鉴定及生物信息学分析，通过qRT-PCR技术检测其在多花黄精不同组织部位及不同浓度NaCl处理下的相对表达量，利用RT-PCR技术构建PcPLT2-2、PcPLT2-7基因融合表达载体，观察其荧光信号验证亚细胞定位。【结果】共鉴定获得15个PcPLT家族成员，该家族无内含子结构，蛋白编码长度为159～601个氨基酸，均为亲水蛋白；进化树分析显示PcPLT与百合科石刁柏（Asparagus officinalis L.）亲缘关系最近；亚细胞定位预测及验证结果显示PcPLT2-2定位于细胞质、细胞核中，PcPLT2-7定位于细胞核中。qRT-PCR结果显示PcPLT2-3和PcPLT2-7在根状茎中表达最高，PcPLT1-3、PcPLT1-4、PcPLT2-7响应盐胁迫调控。【结论】PcPLT不仅具有组织特异性还能提高抗逆性，提示可能作为器官发育调节因子参与多花黄精根状茎膨大的形态建成，为深入研究PLT调控植物根状茎器官生长发育的生物学功能和多花黄精遗传改良奠定基础。
Keyword ：
PLT PLT 基因家族 基因家族 多花黄精 多花黄精 表达分析 表达分析
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| GB/T 7714 | 朱田圆 , 李小利 , 张慧 et al. 多花黄精PLT基因家族的鉴定与表达分析 [J]. | 福建农业学报 , 2023 , 38 (06) : 678-685 . |
| MLA | 朱田圆 et al. "多花黄精PLT基因家族的鉴定与表达分析" . | 福建农业学报 38 . 06 (2023) : 678-685 . |
| APA | 朱田圆 , 李小利 , 张慧 , 班景洁 , 李丹 , 罗彬彬 et al. 多花黄精PLT基因家族的鉴定与表达分析 . | 福建农业学报 , 2023 , 38 (06) , 678-685 . |
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【目的】筛选鉴定多花黄精中氨基酰化酶（aminoacylase 1,ACY1）基因，为多花黄精抗逆基因功能研究奠定基础。【方法】基于多花黄精转录组数据，对多花黄精氨基酰化酶（PcACY1）基因家族进行鉴定，分析基本理化性质、基因结构、保守基序、进化关系等，并采用qRT-PCR验证ACY1家族成员在不同组织器官中和盐胁迫处理下的表达模式。【结果】多花黄精ACY1家族有2个成员，均为亲水蛋白，具有信号肽，无跨膜结构，亚细胞定位预测结果显示2个成员均定位于细胞质中。与植物其他物种ACY1构建进化树发现，其进化特性可分为2类。植物ACY1启动子顺式作用元件预测结果显示，ACY1存在多种激素、胁迫和生长发育相关的响应元件。qRT-PCR分析结果显示，PcACY1成员在多花黄精不同组织器官中的表达水平差异较大且受盐胁迫诱导。【结论】PcACY1在多花黄精生长发育和抵御逆境过程中可能发挥重要作用，这为进一步研究多花黄精ACY1的功能及遗传改良等奠定基础。
Keyword ：
ACY1 ACY1 多花黄精 多花黄精 家族鉴定 家族鉴定 表达分析 表达分析
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| GB/T 7714 | 张慧 , 罗彬彬 , 朱田圆 et al. 多花黄精ACY1基因家族鉴定及其表达分析 [J]. | 福建农业学报 , 2023 , 38 (06) : 666-677 . |
| MLA | 张慧 et al. "多花黄精ACY1基因家族鉴定及其表达分析" . | 福建农业学报 38 . 06 (2023) : 666-677 . |
| APA | 张慧 , 罗彬彬 , 朱田圆 , 班景洁 , 张春渝 , 李小利 et al. 多花黄精ACY1基因家族鉴定及其表达分析 . | 福建农业学报 , 2023 , 38 (06) , 666-677 . |
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Simple Summary The Lachninae is a unique aphid lineage with some particular characteristics. The first complete mitochondrial genome from this subfamily is reported here, with Stomaphis sinisalicis as a representative. The gene arrangement of the new mitogenome differs greatly from the normal gene order of other aphids and insects. The existence of a tandem repeat region in the Lachninae mitogenome may suggest it is probably an ancient feature of aphid mitogenomes. Phylogenetic analysis indicates a basal position of Lachninae within Aphididae. Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
Keyword ：
aphid aphid gene rearrangement gene rearrangement mitogenome mitogenome repeat region repeat region
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| GB/T 7714 | Zhang, Hui , Liu, Qian , Lu, Congcong et al. The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region [J]. | INSECTS , 2021 , 12 (1) . |
| MLA | Zhang, Hui et al. "The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region" . | INSECTS 12 . 1 (2021) . |
| APA | Zhang, Hui , Liu, Qian , Lu, Congcong , Deng, Jun , Huang, Xiaolei . The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region . | INSECTS , 2021 , 12 (1) . |
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Sooty moulds are fungi of economic importance and with unique lifestyle mainly growing on insect honeydew. However, the lack of genomic data hinders investigation of genetic mechanisms underlying their ecological adaptation. With long-read sequencing technology, we generated the genome of Scorias spongiosa, an extraordinary sooty mould fungus associated with honeydew of colony aphids and producing large fruiting bodies. A 24.21 Mb high-quality genome assembly with a N50 length of 3.37 Mb was obtained. The genome contained 7758 protein coding genes, 97.13% of which were homologous to known genes, and approximately 0.29 Mb repeat sequences. Comparative genomics showed S. spongiosa lost relatively more gene families and contained fewer species-specific genes and gene families, with many CAZyme families and sugar transporters reduced or absent. This study not only promotes understanding of the ecological adaptation of sooty moulds, but also provides valuable genomic data resource for future comparative genomic and genetic studies.
Keyword ：
Capnodiales Capnodiales CAZymes CAZymes Genome evolution Genome evolution Long-read sequencing Long-read sequencing Sooty mould Sooty mould
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| GB/T 7714 | Zhang, Hui , Ye, Longqin , Liu, Qian et al. Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi [J]. | GENOMICS , 2021 , 113 (4) : 2189-2198 . |
| MLA | Zhang, Hui et al. "Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi" . | GENOMICS 113 . 4 (2021) : 2189-2198 . |
| APA | Zhang, Hui , Ye, Longqin , Liu, Qian , Huang, Xiaolei . Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi . | GENOMICS , 2021 , 113 (4) , 2189-2198 . |
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Screening Chinese fir (Cunninghamia lanceolata) clones with efficient calcium utilization is an effective strategy to maintain soil fertility and improve their productivity and adaptability to nutrient stress habitats. The calcium content of 17-year-old Chinese fir progenies was measured, and calcium accumulation, distribution, and utilization efficiency were compared to select clones that had high calcium utilization efficiency (CaUE). Significant differences in calcium content and accumulation were observed in different vegetative organs and clones. The highest average calcium content and accumulation were in needles, and the lowest averages were in stems and dead branches. Clone M43 had the highest total calcium accumulation, whereas clone M37 had the lowest. Among the tested clones, the CaUE of the whole tree for M23, M37, and M25 was significantly high, whereas that for M43 was the lowest. The CaUE of stems was the highest in M23 and lowest in M17. Thus, calcium content and accumulation in the vegetative organs are important factors affecting the CaUE of whole trees and stems of different Chinese fir clones. Considering the comprehensive CaUE and bioaccumulation in whole trees and stems, M23, M25, and M10 were clones with high CaUE that should be used in future studies on high-yield plantations.
Keyword ：
Chinese fir Chinese fir nutrient accumulation nutrient accumulation nutrient stress adaptation nutrient stress adaptation plantation plantation productivity productivity utilization efficiency utilization efficiency
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| GB/T 7714 | Zheng, S. S. , Zhang, H. , Guo, H. L. et al. COMPARISON OF CALCIUM ACCUMULATION, DISTRIBUTION, AND USE EFFICIENCY AMONG CHINESE FIR (CUNNINGHAMIA LANCEOLATA (Lamb.) Hook) CLONES [J]. | APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH , 2021 , 20 (2) : 1385-1398 . |
| MLA | Zheng, S. S. et al. "COMPARISON OF CALCIUM ACCUMULATION, DISTRIBUTION, AND USE EFFICIENCY AMONG CHINESE FIR (CUNNINGHAMIA LANCEOLATA (Lamb.) Hook) CLONES" . | APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH 20 . 2 (2021) : 1385-1398 . |
| APA | Zheng, S. S. , Zhang, H. , Guo, H. L. , Ma, X. Q. , Lin, W. J. , Wu, P. F. . COMPARISON OF CALCIUM ACCUMULATION, DISTRIBUTION, AND USE EFFICIENCY AMONG CHINESE FIR (CUNNINGHAMIA LANCEOLATA (Lamb.) Hook) CLONES . | APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH , 2021 , 20 (2) , 1385-1398 . |
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