Explanipedia

Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea Open

Yongfu Tao, Shichao Sun, Chuanzheng Wei, Yifei Wang, Yanbo Wang , et al. · 2025

Cowpea ( Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal …

Enhanced Pore-C with C-Phasing Enables Chromosomal-Scale, Haplotype-Resolved Assembly of Ultra-Complex Genomes Open

Xingtan Zhang, Yibin Wang, Ping Zhao, Xiaofei Zeng, Jiaxin Yu , et al. · 2025

Ultra-complex, repeat-rich polyploids and hybrid genomes with extensive identical-by-descent regions pose a formidable challenge for chromosome-scale, haplotype-resolved assembly, since short-read scaffolding approaches such as Hi-C strugg…

A k-mer-based GWAS approach empowering gene mining in polyploids Open

Xingtan Zhang, Shuai Chen, Xinlong Liu, Shenyang Qu, Yuhan Song , et al. · 2025

Genome-wide association studies (GWAS) serve as a cornerstone for deciphering the genetic architecture of complex traits. However, conventional GWAS tools, predominantly optimized for diploid species, encounter substantial limitations when…

Gap-free, haplotype-resolved genome assembly reveals allele-specific expression and fruit color regulation in coconut Open

Min Chen, Ziqi Ye, Xiaomei Liu, Xingtan Zhang, Yaodong Yang · 2025

Histology-informed spatial domain identification through multi-view graph convolutional networks Open

Huihui Zhang, Jiaxing Chang, Yue Sun, Peipei Hu, Jing Liu , et al. · 2025

Identifying spatial domains is crucial in spatial transcriptomics, yet effectively integrating gene expression, spatial location, and histology remains challenging. We present STESH, a Spatial Transcriptomics clustering method that combine…

RAGA: a reference-assisted genome assembly tool for efficient population-scale assembly Open

Ru-Peng Zhao, Yuhong Luo, Wen‐Zhao Xie, Zu-Wen Zhou, Yong-Qing Qian , et al. · 2025

High-quality reference genomes at the population scale are fundamental for advancing pan-genomic research. However, high-quality genome assembly at the population scale is costly and time-consuming. To overcome these limitations, we develo…

Current status and prospects of super-pangenome studies in plants Open

Xiaoqin Huang, Lisong Hu, Rui Fan, Xingtan Zhang, Chaoyun Hao · 2025

International research initiative on genomics-guided sugarcane breeding Open

Xingtan Zhang, Jungang Wang, Noor‐ul‐Ain, Youxiong Que, Jisen Zhang , et al. · 2025

Genetic Editing of Tomato Golgi-Localized Nucleotide Sugar Transporter 1.1 Promotes Immunity Against Phytophthora infestans Open

Pingping He, Yanling Cai, Yanzi Wang, Zhiqing Wang, Yaqing Lyu , et al. · 2025

Background: Functional alleles of host plant susceptibility genes (S genes) can exacerbate the severity of diseases by enhancing pathogen compatibility. Genetic editing of the targeted host S genes has demonstrated remarkable efficacy in c…

Pan-genome analysis reveals the evolution and diversity of Malus Open

Wei Li, Chong Chu, Taikui Zhang, Haochen Sun, Shiyao Wang , et al. · 2025

Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement Open

Weilong Kong, Xiangrui Kong, Zhongqiang Xia, Xiaofeng Li, Fang Wang , et al. · 2025

Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement Open

Hao Feng, Qingwei Du, Ying Jiang, Yong Jia, Tianhua He , et al. · 2025

The telomere-to-telomere gap-free genome assembly of Juglans sigillata Open

Delu Ning, Tao Wu, Wen‐Long Lei, Shengcheng Zhang, Ting Ma , et al. · 2024

Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness, including essential nutrients, antioxidants, and healthy fats, which boost human cardial, brain and gut health. Despite its importance, the lack …

Collinearity-based Assembly Correction Tool GUI: Software for collinearity-based genome assembly correction Open

Shengcheng Zhang, Hejun Du, Xingtan Zhang, Binzhong Wang · 2024

Genome assembly errors can have a profound effect on downstream analyses. Collinearity-based Assembly Correction Tool GUI is designed to rectify these errors by leveraging collinearity information between the assembled genome and a referen…

The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants Open

Lin Zhang, Shi Yan, Wenfang Gong, Guang Zhao, Shixin Xiao , et al. · 2024

The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants Open

Lin Zhang, Shi Yan, Wenfang Gong, Guang Zhao, Shixin Xiao , et al. · 2024

Camellia oleifera is an economically important woody oil plant. Complex ploidy and lack of genomic information have seriously hindered the molecular breeding of C. oleifera. Here, we present an 11.43-Gb haplotype-resolved, chromosome-level…

JCVI: A versatile toolkit for comparative genomics analysis Open

Haibao Tang, Vivek Krishnakumar, Xiaofei Zeng, Zhou-Geng Xu, Adam Taranto , et al. · 2024

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 …

Comparative Genome-Wide Identification of the Fatty Acid Desaturase Gene Family in Tea and Oil Tea Open

Ziqi Ye, Dan Mao, Yujian Wang, Hongda Deng, Xing Liu , et al. · 2024

Camellia oil is valuable as an edible oil and serves as a base material for a range of high-value products. Camellia plants of significant economic importance, such as Camellia sinensis and Camellia oleifera, have been classified into sect…

A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution Open

Yixue Bao, Qing Zhang, Jiangfeng Huang, Shengcheng Zhang, Wei Yao , et al. · 2024

Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane’s ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. He…

Author Correction: The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence Open

Xiong Huang, Wenling Wang, Ting Gong, David Wickell, Li‐Yaung Kuo , et al. · 2024

Correction to: Nature Plantshttps://doi.org/10.1038/s41477-022-01146-6, published online 9 May 2022. In the version of the article initially published, Dipak Khadka, who collected the samples in Nepal, was thanked in the Acknowledgements i…

Haplotype-resolved genome assembly of Corydalis yanhusuo, a traditional Chinese medicine with unusual telomere motif Open

Ding‐Qiao Xu, Ziqi Ye, Yongji Huang, Kejin Zhu, Hongbo Xu , et al. · 2024

Multi-Type Information Acquisition with Integer Trader Constraints Open

Hui Ou‐Yang, Weili Wu, Xingtan Zhang · 2024

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes Open

Xiaofei Zeng, Zili Yi, Xingtan Zhang, Yuhui Du, Li Yu , et al. · 2023

Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As seque…

Genome sequencing revealed the red-flower trait candidate gene of a peach landrace Open

Ping Zhou, Siru Lei, Xiaodan Zhang, Yinghao Wang, Rui Guo , et al. · 2023

Peach (Prunus persica) is an economically important fruit crop globally and an excellent material for genomic studies. While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives, certa…

The high-resolution three-dimensional (3D) chromatin map of the tea plant (Camellia sinensis) Open

Weilong Kong, Jiaxin Yu, Jingjing Yang, Yanbing Zhang, Xingtan Zhang · 2023

Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes Open

Yinquan Qu, Xulan Shang, Shengzuo Fang, Xingtan Zhang, Xiangxiang Fu · 2023

Cyclocarya paliurus , an endemic species in the genus Juglandaceae with the character of heterodichogamy, is one of triterpene-rich medicinal plants in China. To uncover the genetic mechanisms behind the special characteristics, we sequenc…

Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis Open

Qing Zhang, Ziqi Ye, Yinghao Wang, Xingtan Zhang, Weilong Kong · 2023

The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negativel…

5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.) Open

Weilong Kong, Qiufang Zhu, Qing Zhang, Yiwang Zhu, Jingjing Yang , et al. · 2023

In plants, 5mC DNA methylation is an important and conserved epistatic mark involving genomic stability, gene transcriptional regulation, developmental regulation, abiotic stress response, metabolite synthesis, etc. However, the roles of 5…

A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis Open

Huakun Zheng, Baiyu Wang, Xiuting Hua, Ruiting Gao, Yuhao Wang , et al. · 2023

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 com…

Editorial: Advances in crop biomass production based on multi-omics approach Open

Yin Li, Weizhen Liu, Xingtan Zhang, Shouchuang Wang, Ramin Yadegari , et al. · 2023

EDITORIAL article Front. Plant Sci., 19 April 2023Sec. Plant Bioinformatics Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1155442

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