中国科技期刊卓越行动计划推介：JGG（2025年第1期）

摘要：On the cover: Deciphering spatial domains coherent in gene expression and spatial topology from spatial resolved transcriptomics d

Journal of Genetics and Genomics 2025年第1期(Volume 52, Issue 1, 2025) 在线发表，欢迎大家下载阅读。

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本期封面

Volume 52, Issue 1

On the cover: Deciphering spatial domains coherent in gene expression and spatial topology from spatial resolved transcriptomics data is a critical task. However, existing methods often consider only the spatial location relationship between spots or cells, overlooking other potential biological relationships. In this issue, Sun et al. propose SpaGRA, a method combining graph augmentation and geometric contrastive learning that uses multi-head attention to capture multi-level biological interactions and negative sample generation strategy to enhance robustness (pp. 93–104). The cover image shows three distinct spatial domains, analogous to Cao Wei, Shu Han, and Eastern Wu during the Three Kingdoms period in ancient China (AD 220–280). SpaGRA is capable of effectively capturing the border interactions, such as conﬂict and cooperation, which symbolize the key biological connections among distinctive cell types, signiﬁcantly improving the accuracy of spatial domain identiﬁcation.

本期内容简介

Meeting Report

The future of zebrafish research: highlights from the 18th International Zebrafish Conference

Chenyang Bian, Dongyuan Ma, Feng Liu

中国科学院动物研究所刘峰团队总结第十八届国际斑马鱼大会的最新研究成果，并就斑马鱼领域的未来发展进行展望，强调高分辨率成像技术及多组学技术的广泛应用。

Review

Crop root system architecture in drought response

Yanjun Zhang, Xi Wu, Xingrong Wang, Mingqiu Dai, Yunling Peng

甘肃农业大学彭云玲团队、华中农业大学代明球团队和甘肃省农业科学院作物研究所王兴荣团队联合综述干旱胁迫下作物根系结构的遗传调控网络，概述作物抗旱性的理想根系结构特征，讨论作物根系结构改良策略及其在作物抗旱遗传改良和抗旱育种上面临的挑战以及未来研究方向。

The interplay between extracellular and intracellular auxin signaling in plants

Wenxin Tang, Yongqiang Yu, Tongda Xu

福建农林大学徐通达教授团队综述总结生长素生物学功能特性，介绍了胞外和胞内生长素信号通路的组成，重点阐述了胞外和胞内生长素信号通路在植物多个重要生物学过程中的交互调控作用。

The interplay between histone modifications and nuclear lamina in genome regulation

Chang Sun, Yanjing Zhao, Liping Guo, Juhui Qiu, Qin Peng

深圳湾实验室系统与物理生物学研究所彭琴和重庆大学生物工程学院邱菊辉团队联合综述染色质修饰与核纤层在基因组转录调控中的相互作用，并探讨了它们在细胞分化中的调控作用及在疾病治疗中的潜在应用。

Original Research

KDM2A and KDM2B protect a subset of CpG islands from DNA methylation

Yuan Liu, Ying Liu, Yunji Zhu, Di Hu, Hu Nie, Yali Xie, Rongrong Sun, Jin He, Honglian Zhang, Falong Lu

中国科学院遗传与发育生物学研究所陆发隆研究员团队揭示KDM2A和KDM2B蛋白协同调控哺乳动物基因组中部分CpG岛低甲基化状态的分子机制，为哺乳动物基因组中总体DNA甲基化模式建立与维持提供新见解。

Rab1 and Syntaxin 17 regulate hematopoietic homeostasis through β-integrin trafficking in Drosophila

Fangzhou Luo, Luwei Sui, Ying Sun, Zhixian Lai, Chengcheng Zhang, Gaoqun Zhang, Bing Bi, Shichao Yu, Li Hua Jin

东北林业大学金丽华教授团队揭示了果蝇小GTP酶Rab1和Qa-SNARE蛋白Syx17通过调节β-integrin的囊泡转运维持造血作用稳态，为研究造血干细胞的非自主调节机制提供新思路。

Prox1a promotes liver growth and differentiation by repressing cdx1b expression and intestinal fate transition in zebrafish

Yingying Hu, Zhou Luo, Meiwen Wang, Zekai Wu, Yunxing Liu, Zhenchao Cheng, Yuhan Sun, Jing-Wei Xiong, Xiangjun Tong, Zuoyan Zhu, Bo Zhang

北京大学生命科学学院张博教授团队揭示了Prox1a通过抑制肝脏细胞向肠道命运分化调控斑马鱼肝脏发育的新机制，为理解Prox1在脊椎动物肝脏发育中的关键作用以及探究同源异形盒家族基因间的功能相互作用提供了新思路。

Epigenetic basis for the establishment of ruminal tissue-specific functions in bovine fetuses and adults

Jing Wang, Wen Yuan, Fang Liu, Guangbo Liu, Xiaoxiong Geng, Chen Li, Chenchen Zhang, Nan Li, Xueling Li

内蒙古大学李雪玲研究员团队通过多组学分析揭示牛瘤胃组织特异性差异甲基化区域对其发育和功能建立的调控机制，DNA甲基化可以通过远端增强子调节瘤胃上皮发育及酮体代谢，为反刍动物表观基因组学研究提供新视角。

Method

SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics

Xue Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhiping Liu, Zhiyuan Yuan, Rui Gao

山东大学控制科学与工程学院高瑞教授团队和复旦大学类脑智能科学与技术研究院原致远青年副研究员合作开发了一个新的空间域识别方法SpaGRA (https://github.com/sunxue-yy/SpaGRA)。该方法能够通过图增强算法实现多重关系的自动构建，挖掘SRT数据中细胞间潜在的多层次关系，从而改进空间域的识别效果，为基于SRT的空间结构域预测提供了新的思路(封面论文)。

Improving precision base editing of the zebrafish genome by Rad51DBD-incorporated single-base editors

Zhilin Zhong, Xueli Hu, Renjie Zhang, Xu Liu, Wenqi Chen, Shubin Zhang, Jianjian Sun, Tao P. Zhong

华东师范大学生命科学学院钟涛教授团队构建带有单链DNA结合蛋白Rad51DBD的超高活性胞嘧啶碱基编辑器zhyA3A-CBE5，在斑马鱼中展示出更强的C-T编辑活性和更宽的编辑窗口，在人类遗传疾病点突变的构建方面具有明显优势。该研究扩展了斑马鱼基因组碱基编辑平台，增强了单碱基编辑器在疾病模型和基因功能研究中的应用。

Research Communications

Pan-genome analyses add ∼1000 genes to the “complete” genome assembly of chicken

Jilong Ren, Wenyan Kou, Yuan Xu, Meixuan Lu, Mian Gong, Xinmiao Zhang, Zhenyu Liu, Hengkuan Li, Qimeng Yang, Ali Mujtaba Shah, Feng Zhu, Zhuocheng Hou, Naiyi Xu, Yu Jiang, Fei Wang

西北农林科技大学姜雨教授团队基于鸡GRCg7b和GGswu1两个参考基因组构建更加完善的鸡泛基因组，分别鉴定到了208.1 Mb和170.3 Mb的新序列，注释到1242和880个新基因，为家禽的功能基因组学研究提供更加完整的基因集合。

TaNPF6.2 improves agronomic traits via enhancing nitrogen uptake efficiency in wheat

Huanhuan Wang, Yangyang Liu, Lifen Wu, Chuan Xia, Yaoyu Chen, Xiuying Kong, Feng Shi, Huili Li, Xifang Yang, Liang Ma, Jiaqiang Sun, Lichao Zhang, Zhencheng Xie