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学者姓名：张积森
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The multi-petal "Hutou" jasmine (Jasminum sambac var. Trifoliatum) is highly valued for bonsai cultivation and landscape design, however, the aroma profile and mechanisms underlying floral scent formation remain elusive. In this study, we generate a nearly complete telomere-to-telomere (T2T) genome assembly of "Hutou" jasmine (487.45 Mb with contig N50 of 38.93 Mb). Metabolomic profiling unveils that 16 significantly differential volatiles (SDVs) may play a crucial role in the formation of flower aroma. Among them, five scented SDVs, particularly alpha-farnesene and pentanoic acid 1-ethenyl-1,5-dimethyl-4-hexenyl ester, contribute to the characteristic aroma profile of "Hutou" jasmine flowers. Weighted gene co-expression network analysis (WGCNA) identifies HTWRKY41, HTWRKY53, and HTHSP90 as the hub genes potentially regulating the production of these 16 metabolites. The expression of selected genes and duplication events drive the increased relative content of major sesquiterpenoids in terpenoid biosynthetic pathway. Four structural genes (BEAT3, BSMT1, BPBT2, and BPBT3) are potentially implicated in the emission of downstream key volatile esters (benzyl acetate, methyl benzoate, and benzyl benzoate) in the phenylpropanoids synthesis. Our integrated dataset of genomics, transcriptomics, and metabolomics present here provides a theoretical basis for the practical utilization of fragrance and genetic improvement in horticultural applications of "Hutou" jasmine.
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| GB/T 7714 | Fang, Jingping , Zhou, Linwei , Chen, Qinchang et al. Integrated multi-omics analysis unravels the floral scent characteristics and regulation in "Hutou" multi-petal jasmine [J]. | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
| MLA | Fang, Jingping et al. "Integrated multi-omics analysis unravels the floral scent characteristics and regulation in "Hutou" multi-petal jasmine" . | COMMUNICATIONS BIOLOGY 8 . 1 (2025) . |
| APA | Fang, Jingping , Zhou, Linwei , Chen, Qinchang , Wang, Jinbin , Zhuang, Ying , Lin, Shaoqing et al. Integrated multi-omics analysis unravels the floral scent characteristics and regulation in "Hutou" multi-petal jasmine . | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
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BackgroundSugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular "energy factories", provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS).ResultsWe performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species.ConclusionIn this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.
Keyword ：
Cytoplasmic male sterility (CMS) Cytoplasmic male sterility (CMS) Mitochondrial genome Mitochondrial genome Repeat sequences Repeat sequences Simple sequence repeat (SSR) Simple sequence repeat (SSR) Sugarcane Sugarcane
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| GB/T 7714 | Li, Yihan , Li, Shuangyu , Hua, Xiuting et al. Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane [J]. | BMC GENOMICS , 2025 , 26 (1) . |
| MLA | Li, Yihan et al. "Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane" . | BMC GENOMICS 26 . 1 (2025) . |
| APA | Li, Yihan , Li, Shuangyu , Hua, Xiuting , Xu, Yi , Chen, Shuqi , Yu, Zehuai et al. Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane . | BMC GENOMICS , 2025 , 26 (1) . |
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Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into M alpha, M beta and M gamma subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.
Keyword ：
ABCDE model ABCDE model Flower development Flower development MADS-box genes MADS-box genes Phytohormones Phytohormones Spinach Spinach
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| GB/T 7714 | Fatima, Mahpara , Ma, Xiaokai , Zhang, Jisen et al. Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach [J]. | SCIENTIFIC REPORTS , 2024 , 14 (1) . |
| MLA | Fatima, Mahpara et al. "Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach" . | SCIENTIFIC REPORTS 14 . 1 (2024) . |
| APA | Fatima, Mahpara , Ma, Xiaokai , Zhang, Jisen , Ming, Ray . Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach . | SCIENTIFIC REPORTS , 2024 , 14 (1) . |
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Knowledge of the function of growth-regulating factors (GRFs) in sugarcane ( Saccharum officinarum and S. spontaneum ) growth and development could assist breeders in selecting desirable plant architectures. However, limited information about GRFs is available in Saccharum due to their polyploidy. In this study, 22 GRFs were identified in the two species and their conserved domains, gene structures, chromosome location, and synteny were characterized. GRF7 expression varied among tissues and responded to diurnal rhythm. SsGRF7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional cofactor. SsGRF7 positively regulated the size and length of rice leaves, possibly by regulating cell size and plant hormones. Of seven potential transcription factors binding to the SsGRF7 promoter in S. spontaneum , four showed positive expression patterns, and two showed negative expression patterns relative to SsGRF7 . (c) 2024 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.
Keyword ：
Expression analysis Expression analysis Growth-regulating factor Growth-regulating factor Leaf development Leaf development Sugarcane Sugarcane Transcription factors Transcription factors
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| GB/T 7714 | Wang, Qiaoyu , Li, Yihan , Lin, Dadong et al. A growth-regulating factor 7 ( GRF7 )-mediated gene regulatory network promotes leaf growth and expansion in sugarcane [J]. | CROP JOURNAL , 2024 , 12 (2) : 422-431 . |
| MLA | Wang, Qiaoyu et al. "A growth-regulating factor 7 ( GRF7 )-mediated gene regulatory network promotes leaf growth and expansion in sugarcane" . | CROP JOURNAL 12 . 2 (2024) : 422-431 . |
| APA | Wang, Qiaoyu , Li, Yihan , Lin, Dadong , Feng, Xiaoxi , Wang, Yongjun , Wang, Tianyou et al. A growth-regulating factor 7 ( GRF7 )-mediated gene regulatory network promotes leaf growth and expansion in sugarcane . | CROP JOURNAL , 2024 , 12 (2) , 422-431 . |
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The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python-based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high-level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication-ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability. The JCVI library contains a set of computational tools that are often used in tasks covering genome assembly, annotation, and comparative genomics. Engineered with a focus on versatility, the library incorporates modules for algorithms, format parsing, and graphics generation, enabling seamless integration into diverse research workflows. image JCVI is a Python-based library that enables genomic workflows through a collection of simple reusable tools. The JCVI library is modular with basic functionalities separated into bioinformatics format parsing, assembly and annotation-related tools, comparative genomics, and graphics generation. Embedded algorithms like MCscan, ALLMAPS, and other tools within JCVI are now widely used in the community and power a wide array of use cases.
Keyword ：
comparative genomics comparative genomics genome annotation genome annotation genome assembly genome assembly genomic data genomic data visualization visualization
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| GB/T 7714 | Tang, Haibao , Krishnakumar, Vivek , Zeng, Xiaofei et al. JCVI: A versatile toolkit for comparative genomics analysis [J]. | IMETA , 2024 , 3 (4) . |
| MLA | Tang, Haibao et al. "JCVI: A versatile toolkit for comparative genomics analysis" . | IMETA 3 . 4 (2024) . |
| APA | Tang, Haibao , Krishnakumar, Vivek , Zeng, Xiaofei , Xu, Zhougeng , Taranto, Adam , Lomas, Johnathan S. et al. JCVI: A versatile toolkit for comparative genomics analysis . | IMETA , 2024 , 3 (4) . |
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JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated-2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.
Keyword ：
allotetrapolyploid allotetrapolyploid Cenchrus grass Cenchrus grass centromere architecture centromere architecture evolutionary trajectory evolutionary trajectory genome assembly genome assembly photosyn-thetic efficiency photosyn-thetic efficiency
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| GB/T 7714 | Zheng, Huakun , Wang, Baiyu , Hua, Xiuting et al. A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis [J]. | PLANT COMMUNICATIONS , 2023 , 4 (5) . |
| MLA | Zheng, Huakun et al. "A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis" . | PLANT COMMUNICATIONS 4 . 5 (2023) . |
| APA | Zheng, Huakun , Wang, Baiyu , Hua, Xiuting , Gao, Ruiting , Wang, Yuhao , Zhang, Zixin et al. A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis . | PLANT COMMUNICATIONS , 2023 , 4 (5) . |
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本发明属于植物分子生物学技术及分子检测技术领域，具体涉及一种甘蔗转录因子基因NAC1‑1在蔗茎发育中的应用。所述甘蔗转录因子基因NAC1‑1是从蔗茎绵心的甘蔗品种中克隆得到，其核苷酸序列如SEQ ID NO.1所示，其编码的蛋白质由289个氨基酸残基组成，其中50~150位氨基酸残基为NAC基因家族典型的NAM结构域。本发明揭示NAC1‑1基因的高效表达可诱导蔗茎产生绵心表型，低表达或者不表达没有绵心蔗茎的出现。结果证明，NAC1‑1基因的低表达对于甘蔗蔗茎正常发育具有重要调控作用，也为选育非绵心甘蔗新品种提供了重要理论依据和候选靶标基因资源。
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| GB/T 7714 | 王恒波 , 张积森 , 吴明星 et al. 一种甘蔗转录因子基因NAC1-1在蔗茎发育中的应用 : CN202310566156.5[P]. | 2023-05-19 . |
| MLA | 王恒波 et al. "一种甘蔗转录因子基因NAC1-1在蔗茎发育中的应用" : CN202310566156.5. | 2023-05-19 . |
| APA | 王恒波 , 张积森 , 吴明星 , 黄国强 , 郭晋隆 . 一种甘蔗转录因子基因NAC1-1在蔗茎发育中的应用 : CN202310566156.5. | 2023-05-19 . |
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本发明涉及一种诱导甘蔗茎绵心发育的启动子ProSsNAC1‑1及其应用。所述启动子ProSsNAC1‑1是从蔗茎绵心的甘蔗割手密种中克隆得到，核苷酸序列如SEQ ID NO.1所示。分别将ProSsNAC1‑1和蔗茎实心的甘蔗热带种来源的启动子ProSoNAC1‑1与GUS基因构建融合表达载体，转化拟南芥，将T3代纯合转基因拟南芥植株分别在不同组织及低温和干旱胁迫下进行表达模式分析和组织化学染色。结果证实，启动子ProSsNAC1‑1比ProSoNAC1‑1具有较强的表达量；启动子ProSsNAC1‑1能驱动NAC1‑1基因在甘蔗叶脉和茎秆的维管束组织高效表达，且其受低温和干旱诱导。本发明的启动子ProSsNAC1‑1对甘蔗茎绵心发育调控、甘蔗品质改良具重要价值。
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| GB/T 7714 | 王恒波 , 吴明星 , 张积森 et al. 一种诱导甘蔗茎绵心发育的启动子及其应用 : CN202310567324.2[P]. | 2023-05-19 . |
| MLA | 王恒波 et al. "一种诱导甘蔗茎绵心发育的启动子及其应用" : CN202310567324.2. | 2023-05-19 . |
| APA | 王恒波 , 吴明星 , 张积森 , 黄国强 , 郭晋隆 . 一种诱导甘蔗茎绵心发育的启动子及其应用 : CN202310567324.2. | 2023-05-19 . |
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目前芦竹属(Arundo)菌草形态学的鉴定方法已经建立，但是在分子水平上的研究较少。对芦竹属菌草进行分子鉴定与选择压力分析可为菌草的杂交育种奠定基础。本研究通过PCR扩增得到芦竹属菌草的ITS2基因序列，并对它们的叶片进行转录组测序，通过生物信息学方法对其进行分子鉴定与选择压力分析。结果表明：在6.21百万年-9.75百万年前，以及5.14百万年-8.07百万年前分别进行了两次大规模的分化，将它们分为3大类(‘绿洲3号’‘绿洲5号’‘绿洲6号’‘绿洲8号’、‘绿洲2号’‘绿洲4号’‘绿洲7号’‘绿洲12号’和其他菌草)。选择压力分析筛选出‘绿洲1号’和‘绿洲3号’的正选择基因，它们大部分与转录调控、抗逆与发育相关。研究结果揭示了芦竹属菌草品种之间的关系和受到正向选择的基因与位点，为芦竹属菌草的适应性进化提供见解，也为今后的遗传改良提供靶点。
Keyword ：
ITS2序列 ITS2序列 分歧时间 分歧时间 系统发育 系统发育 芦竹 芦竹 转录组 转录组 选择压力 选择压力
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| GB/T 7714 | 孙源长 , 王天友 , 罗琳 et al. 芦竹属菌草的分子鉴定及适应性进化分析 [J]. | 草业科学 , 2023 , 40 (06) : 1568-1581 . |
| MLA | 孙源长 et al. "芦竹属菌草的分子鉴定及适应性进化分析" . | 草业科学 40 . 06 (2023) : 1568-1581 . |
| APA | 孙源长 , 王天友 , 罗琳 , 蔡杨星 , 林辉 , 林冬梅 et al. 芦竹属菌草的分子鉴定及适应性进化分析 . | 草业科学 , 2023 , 40 (06) , 1568-1581 . |
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BackgroundJute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress.ResultsIn the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants.ConclusionsThis study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.
Keyword ：
CCoAOMT CCoAOMT Evolution Evolution Expression Expression Jute Jute Lignin Lignin
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| GB/T 7714 | Kahie, Mohamed Ali , Wang, Yongjun , Fang, Pingping et al. Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.) [J]. | BMC GENOMICS , 2023 , 24 (1) . |
| MLA | Kahie, Mohamed Ali et al. "Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.)" . | BMC GENOMICS 24 . 1 (2023) . |
| APA | Kahie, Mohamed Ali , Wang, Yongjun , Fang, Pingping , Qi, Jianmin , Lei, Rongjie , Xu, Jiantang et al. Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.) . | BMC GENOMICS , 2023 , 24 (1) . |
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