Journal of Genetics and Genomics2025年第1期(Volume 52, Issue 1, 2025) 在线发表，接待公共下载阅读。
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https://www.sciencedirect.com/journal/journal-of-genetics-and-genomics/vol/52/issue/1
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.
本期执行简介
Volume 52, Issue 1
Meeting Report
The future of zebrafish research: highlights from the 18th International Zebrafish Conference
Chenyang Bian, Dongyuan Ma, Feng Liu
https://doi.org/10.1016/j.jgg.2024.09.006
中国科学院动物研究所刘峰团队纪念第十八届国外斑马鱼大会的最新研究收尾，并就斑马鱼限制的改日发展进行臆测，强调高分辨率成像时刻及多组学时刻的庸俗专揽。
Review
Crop root system architecture in drought response
Yanjun Zhang, Xi Wu, Xingrong Wang, Mingqiu Dai, Yunling Peng
https://doi.org/10.1016/j.jgg.2024.05.001
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调和综述干旱威迫下作物根系缚构的遗传调控收集，概括作物抗旱性的空想根系缚构特征，野心作物根系缚构矫正计谋过甚在作物抗旱遗传矫正和抗旱育种上靠近的挑战以及改日研究标的。
The interplay between extracellular and intracellular auxin signaling in plants
Wenxin Tang, Yongqiang Yu, Tongda Xu
https://doi.org/10.1016/j.jgg.2024.06.019
福建农林大学徐表示西宾团队综述纪念滋长素生物学功能特点，先容了胞外和胞内滋长素信号通路的构成，重心阐述了胞外和胞内滋长素信号通路在植物多个紧要生物学历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
https://doi.org/10.1016/j.jgg.2024.10.005
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调和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，并辩论了它们在细胞分化中的调控作用及在疾病调整中的潜在专揽。
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
https://doi.org/10.1016/j.jgg.2024.10.012
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卵白协同调控哺乳动物基因组中部分CpG岛低甲基化情状的分子机制，为哺乳动物基因组中总体DNA甲基化方式设备与看守提供新想法。
Rab1 and Syntaxin 17 regulate hematopoietic homeostasis through β-integrin trafficking inDrosophila
Fangzhou Luo, Luwei Sui, Ying Sun, Zhixian Lai, Chengcheng Zhang, Gaoqun Zhang, Bing Bi, Shichao Yu, Li Hua Jin
https://doi.org/10.1016/j.jgg.2024.11.001
东北林业大学金丽华西宾团队揭示了果蝇小GTP酶Rab1和Qa-SNARE卵白Syx17通过转机β-integrin的囊泡转运看守造血作用稳态，为研究造血干细胞的非自主转机机制提供新念念路。
Prox1a promotes liver growth and differentiation by repressingcdx1bexpression 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
https://doi.org/10.1016/j.jgg.2024.09.010
北京大学人命科学学院张博西宾团队揭示了Prox1a通过阻止肝脏细胞向肠说念气运分化调控斑马鱼肝脏发育的新机制，为意会Prox1在脊椎动物肝脏发育中的要道作用以及探究同源异形盒家眷基因间的功能相互作用提供了新念念路。
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
https://doi.org/10.1016/j.jgg.2024.10.008
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互异甲基化区域对其发育和功能设备的调控机制，DNA甲基化不错通过远端增强子转机瘤胃上皮发育及酮体代谢，AG百家乐有没有追杀为反刍动物表不雅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
https://doi.org/10.1016/j.jgg.2024.09.015
山东大学截至科学与工程学院高瑞西宾团队和复旦大学类脑智能科学与时刻研究院原致远后生副研究员互助开发了一个新的空间域识别门径SpaGRA (
https://github.com/sunxue-yy/SpaGRA)。该门径简略通过图增强算法已毕多重计划的自动构建，挖掘SRT数据中细胞间潜在的多档次计划，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念念路(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
https://doi.org/10.1016/j.jgg.2024.10.006
华东师范大学人命科学学院钟涛西宾团队构建带有单链DNA劝诱卵白Rad51DBD的超高活性胞嘧啶碱基裁剪器zhyA3A-CBE5，在斑马鱼中展示出更强的C-T裁剪活性和更宽的裁剪窗口，在东说念主类遗传疾病点突变的构建方面具有昭着上风。该研究膨胀了斑马鱼基因组碱基裁剪平台，增强了单碱基裁剪器在疾病模子和基因功能研究中的专揽。
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
https://doi.org/10.1016/j.jgg.2024.10.009
西北农林科技大学姜雨西宾团队基于鸡GRCg7b和GGswu1两个参考基因组构建愈加完善的鸡泛基因组，阔别轻薄到了208.1 Mb和170.3 Mb的新序列，注目到1242和880个新基因，为家禽的功能基因组学研究提供愈加竣工的基因调和。
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
https://doi.org/10.1016/j.jgg.2024.11.004
中国农业科学院作物科学研究所小麦产量性状理会与想象团队理会TaNPF6.2通过升迁小麦氮素吸告成率改善农艺性状(如加多分蘖数、穗长、穗粒数和千粒重等)的分子机制，为小麦绿色高产育种提供了新的候选基因。
Zebrafish cartilage development atlas generated by longitudinal in vivo imaging
Shirong Jin, Hongfei Zhang, Jia Li, Huaxing Zi, Jiulin Du, Hongyu Li
https://doi.org/10.1016/j.jgg.2024.11.003
中国科学院脑科学与智能时刻不凡革命中心杜久林研究员团队通过秀雅内源性皆集卵白聚糖A (Aggrecan A, acana)AG百家乐到底是真是假，构建了斑马鱼年少期全身软骨发育图谱，为研究软骨发育提供了可视化资源。