Article
Agricultural Engineering
Ruisen Lu, Min Chen, Yu Feng, Na Yuan, Yanmei Zhang, Minxu Cao, Jia Liu, Yue Wang, Yueyu Hang, Xiaoqin Sun
Summary: This study used a genome skimming strategy to retrieve plastome information of Zizania and identify polymorphic nuclear SSRs within this genus. The findings provide genetic resources for further research and commercial exploitation of this economically significant crop.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Matteo Martina, Alberto Acquadro, Lorenzo Barchi, Davide Gulino, Fabio Brusco, Mario Rabaglio, Flavio Portis, Ezio Portis, Sergio Lanteri
Summary: This study obtained the first draft genome of Anemone coronaria and developed a set of microsatellite markers specific for this species. The results of this study provide valuable tools for Breeding Rights disputes, breeding strategies, and phylogenetic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study sequenced and analyzed the chloroplast genomes of 13 Eragrostideae species, identifying useful molecular markers for phylogenetic analysis. The study revealed Enneapogon as the earliest diverging lineage, Eragrostis as the sister to Uniola including Harpachne, and discussed the classification of Harpachne harpachnoides based on morphological and molecular evidence.
Article
Genetics & Heredity
Zinian Wu, Chunyu Tian, Yanting Yang, Yuanheng Li, Qian Liu, Zhiyong Li, Ke Jin
Summary: Leymus is a perennial genus with adaptive capacity and strong resistance to cold, drought, and salinity. The complete chloroplast genomes of Leymus species were sequenced and compared to clarify the taxonomy confusion within the genus.
Article
Biochemistry & Molecular Biology
Xiaoyan Li, Mengyao Li, Weilong Li, Jin Zhou, Qiuju Han, Wei Lu, Qin Luo, Shunhua Zhu, Aisheng Xiong, Guofei Tan, Yangxia Zheng
Summary: This study identified the mitochondrial genomes of Apium graveolens and Apium leptophyllum using different sequencing platforms. It revealed specific gene coding preferences, RNA editing types, and homologous sequences in these two species. These findings provide important data for genetic and evolutionary research in the Apium genus, as well as for comparative genomic analysis in other species within the Apiaceae family.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Sajjad Asaf, Waqar Ahmad, Ahmed Al-Harrasi, Abdul Latif Khan
Summary: The study sequenced and analyzed the complete chloroplast genome of Ziziphus hajarensis, revealing its genetic features and providing insights into its evolution and phylogenetic position among Rhamnaceae species.
Article
Genetics & Heredity
Yinqiao Jian, Wenyuan Yan, Jianfei Xu, Shaoguang Duan, Guangcun Li, Liping Jin
Summary: This study analyzed the abundance and distribution of SSRs in four potato genomes, identifying a large number of polymorphic markers, with a focus on intergenic regions. The high-density potato SSR markers developed will facilitate genetic research and marker-pyramiding in potato breeding.
Article
Agronomy
Shivani Rohilla, Harish S. Ginwal, Vikas Rana, Santan Barthwal, Rajendra K. Meena
Summary: The study developed genome sequence information and novel SSRs for D. strictus, identified a large number of microsatellite repeats, and validated polymorphic SSR markers through PCR amplification. The reliable results from the analysed individuals suggest the potential of these SSRs in improving our understanding of the genomic background of D. strictus.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Mohanad A. Ibrahim, Badr M. Al-Shomrani, Sultan N. Alharbi, Tyler A. Elliott, Mohammed S. Alsuabeyl, Fahad H. Alqahtani, Manee M. Manee
Summary: This study conducted a genome-wide comparative analysis of transposable elements (TEs) in four palm species, revealing the proportion and distribution of TEs in the genomes of these species. The research found significant differences in the abundance of different types of TEs among the studied palm species.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2021)
Article
Biochemistry & Molecular Biology
Maizura Ithnin, Wendy T. Vu, Min-Gyoung Shin, Vasantika Suryawanshi, Katrina Sherbina, Siti Hazirah Zolkafli, Norhalida Mohamed Serdari, Mohd Din Amiruddin, Norziha Abdullah, Suzana Mustaffa, Marhalil Marjuni, Rajanaidu Nookiah, Ahmad Kushairi, Paul Marjoram, Sergey Nuzhdin, Peter L. Chang, Rajinder Singh
Summary: The study reveals genetic similarity between wild American oil palm populations and some cultivated African oil palm populations, potentially originating from the Amazon Basin. Despite genetic bottleneck and inbreeding, there is significant genetic and phenotypic variation for agronomically valuable traits.
Article
Plant Sciences
Vincent Okelo Wanga, Xiang Dong, Millicent Akinyi Oulo, Elijah Mbandi Mkala, Jia-Xin Yang, Guy Eric Onjalalaina, Moses Kirega Gichua, Paul Muigai Kirika, Robert Wahiti Gituru, Guang-Wan Hu, Qing-Feng Wang
Summary: The study investigated the complete chloroplast genome of the Chinese endemic Acanthochlamys bracteata and compared it with African Xerophyta species, revealing genetic relationships and genomic characteristics. Variations were found in gene number, repeat sequences, and nucleotide diversity among the species, providing insights for genetic variability and evolutionary studies in Velloziaceae.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Mariana de Lima Santos, Mario Lucio Vilela de Resende, Gabriel Sergio Costa Alves, Jose Carlos Huguet-Tapia, Marcio Fernando Ribeiro de Resende Junior, Jeremy Todd Brawner
Summary: This study conducted a genome-wide analysis of NLR loci in coffee species and found a rich set of NLR genes. These genes are mainly clustered on chromosomes and shared some orthologous genes with other plants like tomato and potato. The NLR family in coffee is divided into TIR-NLR and non-TIR-NLR, with the non-TIR-NLRs playing an important role in disease resistance. These findings will contribute to functional studies and breeding of disease-resistant coffee cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Ning Chen, Li-Na Sha, Yi-Ling Wang, Ling-Juan Yin, Yue Zhang, Yi Wang, Dan-Dan Wu, Hou-Yang Kang, Hai-Qin Zhang, Yong-Hong Zhou, Gen-Lou Sun, Xing Fan
Summary: The study comprehensively analyzed chloroplast genome variation in 34 monogenomic Triticeae plants, identifying factors such as indels, gene loss, and size variation in different genera. Results suggest that the size and evolution of chloroplast genomes in Triticeae are highly variable and likely influenced by adaptive processes. Additionally, unique genetic information in specific intergenic regions can serve as important tools for identifying maternal relationships among Triticeae species.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agricultural Engineering
Yang Xu, Cuiyu Liu, Xu Yang, Kaiyun Wu, Bangchu Gong
Summary: This study characterized the genome-wide microsatellites in D. oleifera and developed polymorphic SSR markers for Diospyros lotus and Diospyros kaki. A total of 330,507 SSRs were identified from the D. oleifera genome, with an average density of 385.95 SSRs per Mb. Mononucleotide repeats were the most abundant in the genome, while trinucleotide repeats were the most abundant in the coding regions.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Erkui Yue, Hua Tao, Jianhong Xu
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in post-transcriptional gene regulation. One miRNA identified in plants, miR156, targets the SPL transcription factors, which are conserved across species in the grass family. Analysis revealed differential expression patterns of SPLs in different rice tissues and suggested that non-miR156-targeted SPLs may diversify into miR156-targeted genes.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2021)
Article
Plant Sciences
Yi Wang, Haiping Xin, Peige Fan, Jisen Zhang, Yongbo Liu, Yang Dong, Zemin Wang, Yingzhen Yang, Qing Zhang, Ray Ming, Gan-Yuan Zhong, Shaohua Li, Zhenchang Liang
Summary: Vitis amurensis (Shanputao), the most cold-tolerant species of grape, has a genome assembly revealing a common ancestor with V. vinifera and potential gene expansions contributing to cold tolerance. Transcriptome analysis identified 17 genes involved in cold signal transduction with different mechanisms for low temperature and freezing responses. A genome-wide association study highlighted a phosphoglycerate kinase gene implication in winter bud freezing resistance.
Article
Mathematical & Computational Biology
Jiaxuan Li, Shuai Yang, Xiaojie Yang, Hui Wu, Heng Tang, Long Yang
Summary: The Plant Gene Family Platform (PlantGF) is a comprehensive platform for querying and analyzing plant gene families, providing a wide range of functions and tools. It is the first of its kind and will contribute significantly to plant gene family-related research.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Genetics & Heredity
Yalin Zheng, Yudong Chen, Zhiguo Liu, Hui Wu, Fangchan Jiao, Haiping Xin, Li Zhang, Long Yang
Summary: Nicotiana alata, an ornamental horticultural plant, displays a variety of flower colors and a long flowering period. Differences in flower color are explained by analyzing genes in different colored flowers, with crucial roles played by chlorophyll and anthocyanin biosynthesis pathways. Specific genes such as HEMA, F3H, F3 ' 5 ' H, DFR, FLS as well as transcription factor genes like HY5, MYB12, AN1 and AN4, are involved in determining the flower color differences.
Article
Agronomy
Yudong Chen, Shuai Yang, Jiaxuan Li, Kesu Wei, Long Yang
Summary: This study identified a large number of potential resistance genes in six Nicotiana species, indicating the potential abundance of resistance genes in Nicotiana. Additionally, the analysis of pathogen genome sequences revealed high variability and biodiversity among biotic pathogens. To support resistance research, a user-friendly Nicotiana Resistance Database (NRD) was developed.
Article
Biology
Hui Wu, Zixian Wu, Yuanheng Wang, Jie Ding, Yalin Zheng, Heng Tang, Long Yang
Summary: The study focused on the transcriptome and metabolome responses of Camellia sinensis under freezing stress, revealing the critical role of Pyr/PYL-PP2C-SnRK2 pathway and three metabolic pathways in enhancing freezing resistance of C. sinensis. The findings provide important insights for breeding programs to improve freezing tolerance of C. sinensis.
Review
Microbiology
Yudong Chen, Jianfeng Du, Yang Li, Heng Tang, Ziyi Yin, Long Yang, Xinhua Ding
Summary: Continuous cropping has a significant impact on crop yield and quality, including deterioration of soil properties, changes in soil microbial community structure, accumulation of autotoxins, weakened plant growth, and increased diseases and pests. This review summarizes the evolutionary trend of soil microbial structure driven by continuous cropping, and introduces measures and strategies for reshaping the structure.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Weibo Geng, Yanan Wang, Jing Zhang, Zhonghui Liu, Xingyun Chen, Liting Qin, Long Yang, Heng Tang
Summary: This study systematically investigated the NtLEA gene family in tobacco and identified 123 NtLEA genes, which were analyzed in detail. The study found that these genes showed significant induced expression under two different abiotic stresses and exhibited different expression patterns. Additionally, the majority of NtLEA proteins were shown to have the potential function to enhance tobacco resistance to abiotic stress.
Article
Plant Sciences
Yi Wang, Limin Lu, Jingrui Li, Huayang Li, Yichen You, Shuying Zang, Yongqing Zhang, Jianfei Ye, Zemin Lv, Zhaoyu Zhang, Yongsheng Qin, Hongling Zhang, Fei Xia, Hui Li, Huijin Zhang, Peige Fan, Lei Shi, Zhenchang Liang, Hongxia Cui
Summary: Lilacs (Syringa L.) are a well-known group of ornamental and aromatic woody plants that have been extensively used for gardening, essential oils, and medicine in East Asia and Europe. This study presents the chromosome-level genome of Syringa oblata, revealing its evolutionary analysis, transcriptomics, and metabolic profiling. The results provide insights into the origin and diversity of lilacs.
Article
Genetics & Heredity
Kangkang Song, Bin Li, Hui Wu, Yuxue Sha, Liting Qin, Xingyun Chen, Ying Liu, Heng Tang, Long Yang
Summary: B-box (BBX) is a zinc finger transcription factor that plays a crucial role in regulating plant growth and development, as well as stress responses. This study identified and categorized 43 NtBBX genes into five subgroups in tobacco. Promoter analysis revealed that these genes contain cis-acting elements associated with light response, hormone regulation, and stress response. Transcriptome analysis further demonstrated the differential expression of NtBBX genes under abiotic stresses and Ralstonia solanacearum infection. The findings of this study provide valuable insights into the biological functions of NtBBX genes in tobacco.
Article
Plant Sciences
Haiping Xin, Yi Wang, Qingyun Li, Tao Wan, Yujun Hou, Yuanshuang Liu, Duncan Kiragu Gichuki, Huimin Zhou, Zhenfei Zhu, Chen Xu, Yadong Zhou, Zhiming Liu, Rongjun Li, Bing Liu, Limin Lu, Hongsheng Jiang, Jisen Zhang, Junnan Wan, Rishi Aryal, Guangwan Hu, Zhiduan Chen, Robert Wahiti Gituru, Zhenchang Liang, Jun Wen, Qingfeng Wang
Summary: This study provides a chromosomal-level assembly of Cissus rotundifolia and compares it with the grape genome, shedding light on the genome divergence within the ancient eudicot family. The findings highlight the genetic basis underlying C. rotundifolia's adaptation to arid environments and reveal the significant functional divergence from grape.
HORTICULTURE RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Haozhen Li, Kangkang Song, Xiaohua Zhang, Di Wang, Shaolin Dong, Ying Liu, Long Yang
Summary: Tea plants are an economically important crop, and research on tea breeding plays a crucial role in improving yield and quality of tea leaves to meet public demand. This study focuses on the status of tea plants germplasm resources and their utilization, particularly in the application of multi-omics techniques such as genomics and transcriptomics in breeding. It also proposes various molecular markers and approaches for breeding tea plants with high yield, quality, and resistance, as well as future directions involving single-cellomics, pangenomics, plant-microbe interactions, and epigenetics in tea plant breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Huayang Li, Yongbo Liu, Peige Fan, Zhanwu Dai, Jiachen Hao, Wei Duan, Zhenchang Liang, Yi Wang
Summary: This study provides a high-quality chromosome-level reference genome of Vitis zhejiang-adstricta and reveals its evolutionary relationship with East Asian Vitis and the expansion of gene families associated with disease resistance. The near-complete and accurate diploid V. zhejiang-adstricta reference genome obtained in this study serves as an invaluable genomic resource for further investigation of the genomic architecture of V. zhejiang-adstricta and improvement of disease resistance breeding strategies in grape.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Genetics & Heredity
Yi Wang, Jun Xie, Hongna Zhang, Weidong Li, Zhanjun Wang, Huayang Li, Qian Tong, Gaixia Qiao, Yujuan Liu, Ying Tian, Yongzan Wei, Ping Li, Rong Wang, Weiping Chen, Zhengchang Liang, Meilong Xu
Summary: This study obtained the whole genome sequences of Prunus humilis and found that it shares the same ancestor with Prunus mume and Prunus armeniaca. Gene expansion analysis indicated the potential association between gene expansion and drought tolerance in P. humilis. Population diversity analysis revealed limited genetic diversity in P. humilis populations, highlighting the need for collection and utilization of more wild resources.
Article
Horticulture
Guangzhao Xu, Yi Wang, Chong Ren, Peige Fan, Yangfu Kuang, Yue Wang, Zhenchang Liang
Summary: It was found through research that VvGH9 is a gene that can promote sugar accumulation in plants under low sugar content conditions, with its highest expression level in the early fruit stage and being induced by exogenous sugar. The overexpression of VvGH9 in grape calli and tomatoes also confirmed this function.
Article
Plant Sciences
Zemin Wang, Darren Chern Jan Wong, Yi Wang, Guangzhao Xu, Chong Ren, Yanfei Liu, Yangfu Kuang, Peige Fan, Shaohua Li, Haiping Xin, Zhenchang Liang
Summary: The study confirmed that overexpression of VaPAT1 in transformed grape calli enhances cold tolerance, and revealed an interaction between VaPAT1 and VaIDD3, which coordinately modulate the expression of stress-related genes, including the key jasmonate biosynthesis enzyme gene LOX3.