On the cover: Pear is an important fruit tree including five main cultivated species. Owing to self-incompatibility, new pear cultivars are mainly developed via cross-breeding. However, the genomic mechanism underlying heterosis in pear breeding remains unclear. In this issue, Li et al. (2024) report the haplotype-resolved T2T genome assemblies for two pear hybrid varieties and the first pangenome graph for pear. They resolved allele-specific expression (ASE) of genes associated with fruit quality traits and identified structural variant hotspots and selective sweeps during pear domestication and diversification, providing evidence suggesting the contributions of ASE to heterosis in fruit-quality traits.Issue: Plant Communications(cell.com)
Correspondences
The haplotype-resolved T2T genome assemblyof the wild potato species Solanum commersoniiprovides molecular insights into its freezing tolerance
DOI: 10.1016/j.xplc.2024.100980
Yang Feng, Jie Zhou, Dianjue Li, Zhen Wang, Cheng Peng, and Guangtao Zhu
lcQTH: Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing
DOI: 10.1016/j.xplc.2024.101008Wenxi Wang, Zhe Chen, Zhengzhao Yang, Zihao Wang, Jilu Liu,Jie Liu, Huiru Peng, Zhenqi Su, Zhongfu Ni, Qixin Sun,and Weilong Guo
The complete telomere-to-telomere genome assembly of lettuceDOI: 10.1016/j.xplc.2024.101011
Ke Wang, Jingyun Jin, Jingxuan Wang, Xinrui Wang, Jie Sun, Dian Meng, Xiangfeng Wang, Yong Wang, and Li Guo
CentIER: Accurate centromere identification for plant genomesDOI: 10.1016/j.xplc.2024.101046
Dong Xu, Jinbao Yang, Huaming Wen, Wenle Feng, Xiaohui Zhang, Xingqi Hui, Junyang Yue, Yun Xu, Fei Chen, and Weihua Pan
Resource articles
TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybeanDOI: 10.1016/j.xplc.2024.101010
Delin Li, Qi Wang, Yu Tian, Xiangguang Lyv, Hao Zhang, Huilong Hong, Huawei Gao, Yan-Fei Li, Chaosen Zhao, Jiajun Wang, Ruizhen Wang, Jinliang Yang, Bin Liu, Patrick S. Schnable, James C. Schnable, Ying-Hui Li, and Li-Juan Qiu
PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant speciesDOI: 10.1016/j.xplc.2024.101038Yue Hu, Yao Ruan, Xin-Le Zhao, Feng Jiang, Dongxu Liu, Qiang Zhu, Qing-Ye Zhang, and Qing-Yong Yang
Review articles
Crosstalk between RNA m6A modification and epigenetic factors in plant gene regulationDOI: 10.1016/j.xplc.2024.101037Jianzhong Hu, Tao Xu, and Hunseung Kang
Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate changeDOI: 10.1016/j.xplc.2024.101044
Jiajun Feng, Xuming Dan, Yangkai Cui, Yi Gong, Minyue Peng, Yupeng Sang, Par K. Ingvarsson, and Jing Wang四川大学王婧课题组阐述了将进化基因组学研究手段与基因编辑和基因组选择育种技术相结合，以加速培育适应未来气候的林木新种质的巨大潜力。
Research articles
OsNLP3 enhances grain weight and reduces grain chalkiness in riceDOI: 10.1016/j.xplc.2024.100999
Liang-Qi Sun, Yu Bai, Jie Wu, Shi-Jun Fan, Si-Yan Chen,Zheng-Yi Zhang, Jin-Qiu Xia, Shi-Mei Wang, Yu-Ping Wang, Peng Qin, Shi-Gui Li, Ping Xu, Zhong Zhao, Cheng-Bin Xiang,and Zi-Sheng Zhang
Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traitsDOI: 10.1016/j.xplc.2024.101000Qionghou Li, Xin Qiao, Lanqing Li, Chao Gu, Hao Yin, Kaijie Qi, Zhihua Xie, Sheng Yang, Qifeng Zhao, Zewen Wang, Yuhang Yang, Jiahui Pan, Hongxiang Li, Jie Wang, Chao Wang,Loren H. Rieseberg, Shaoling Zhang, and Shutian Tao南京农业大学张绍铃院士团队基于亲本的遗传信息组装了两个杂交选育的梨品种‘玉露香梨’（YLX)和‘红香酥’（HXS）的单倍型T2T基因组，并构建了首个梨泛基因组图谱，揭示了等位基因特异性表达对杂种优势和果实品质性状形成的贡献。Plant Com | 南京农大张绍铃院士团队构建梨T2T基因组和泛基因组图谱揭示等位基因在杂种优势和品质形成中的作用
A KNOX Ⅱ transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in riceDOI: 10.1016/j.xplc.2024.101001Siliang Xu, Xinghua Wei, Qinqin Yang, Dongxiu Hu, Yuanyuan Zhang, Xiaoping Yuan, Fengyu Kang, Zhaozhong Wu, Zhiqin Yan, Xueqin Luo, Yanfei Sun, Shan Wang, Yue Feng, Qun Xu, Mengchen Zhang, and Yaolong Yang中国水稻研究所魏兴华团队利用全基因组关联分析鉴定了一个水稻稻瘟病抗性基因BRG8，并通过遗传学及生理生化实验揭示其抗病分子机制。
GhATL68b regulates cotton fiber cell development by ubiquitinating the enzyme required for b-oxidation of polyunsaturated fatty acidsDOI: 10.1016/j.xplc.2024.101003Xin Li, Gai Huang, Yifan Zhou, Kun Wang, and Yuxian Zhu武汉大学朱玉贤院士发现纤维特异E3泛素连接酶GhATL68b通过调节多不饱和脂肪酸（PUFAs）代谢中限速酶的稳态影响棉纤维细胞发育。本研究揭示了GhATL68b介导的蛋白质降解系统通过调节PUFAs稳态在调控纤维细胞发育中发挥重要作用。这是棉花研究中首次深入解析的C3H2C3型E3泛素连接酶，为提高棉纤维长度和产量提供了一个新的候选遗传改良靶标。
LAZY4 acts additively with the starch–statolith dependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in riceDOI: 10.1016/j.xplc.2024.100943Wenguang Wang, Linzhou Huang, Yuqi Song, Songtao Gui, Jiajia Cao, Han Zhang, Mengchen Du, Jiaze Chen, Zihao Wang,Jie Zhou, Xiangbing Meng, Dali Zeng, Jiayang Li, and Yonghong Wang山东农业大学王永红教授课题组鉴定到一个新的水稻分蘖角度调控基因该研究不仅拓宽了对水稻重力感应机制和分蘖角度遗传调控网络的认识，还为进一步解析不依赖于淀粉平衡石的水稻重力感应和分蘖角度调控机制奠定了基础。
Plant Com | 山东农业大学王永红课题组鉴定到一个新的水稻分蘖角度调控基因
The biosynthesis of asiaticoside and madecassoside reveals tandem duplication–directed evolution of glycoside glycosyltransferases in the Apiales
DOI: 10.1016/j.xplc.2024.101005
Xiaoyang Han, Jingyi Zhao, Hong Zhou, Xuan Zhou, Zixin Deng, Zhenhua Liu, and Yi Yu武汉大学药学院虞沂课题组联手上海交通大学农业与生物学院刘振华教授团队报道了伞形目药用植物积雪草（Centella asiatica）中三萜皂苷天然产物积雪草苷（Asiaticoside）及羟基积雪草苷（Madecassoside）的C-28位G-G-R糖链的生物合成途径与相关酶催化机理。Plant Com | 虞沂课题组和刘振华教授团队合作揭示积雪草苷和羟基积雪草苷C-28位G-G-R糖链的生物合成途径
A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in YuxingcaoDOI: 10.1016/j.xplc.2024.101075
Yuxingcao Zhengting Yang, Fayin He, Yingxiao Mai, Sixian Fan, Yin An, Kun Li, Fengqi Wu, Ming Tang, Hui Yu, Jian-Xiang Liu, and Rui Xia贵州师范大学生命科学学院及西南喀斯特山区生物多样性保护国家林业局重点实验室的杨正婷团队，联合华南农业大学园艺学院的夏瑞教授和浙江大学丽水生命健康创新中心的刘建祥教授成功组装了一个高质量的四倍体鱼腥草基因组（2.24 Gb，76条染色体，4n = 76），并成功拼接了72条染色体的端粒。该研究为深入理解鱼腥草的基因组特征及其黄酮类化合物的生物合成调控机制提供了新的见解，对鱼腥草的药用开发具有重要意义。
Plant Com | 贵州师范大学杨正婷团队联合华南农业大学夏瑞和浙江大学刘建祥团队揭示鱼腥草基因组和黄酮生物合成的调控机制
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