Pineapple, an important tropical herbaceous fruit tree, is renowned for its juicy composite fruits and distinctive aroma. Its extensive evolutionary history, primarily driven by vegetative propagation, has led to a highly heterozygous genome that has been difficult to fully resolve. Here, Feng et al. (pages 2208–2225) have successfully assembled the first telomere-to-telomere genome of pineapple, accompanied by a meticulously curated, highquality gene structure annotation. These comprehensive genomic resources provide a complete map for postgenomic research and breeding efforts in pineapple. The cover image features a flowering hybrid F1 plant, the result of a cross between BL and LY, two pineapple varieties used in the study.

Brief Communications

Efficient and transformation-free genome editing in pepper enabled by RNA virus-mediated delivery of CRISPR/Cas9

Chenglu Zhao, Huanhuan Lou, Qian Liu, Siqi Pei, Qiansheng Liao, Zhenghe Li

Tomato spotted wilt virus-mediated delivery of CRISPR/Cas9 bypasses the need for stable transformation and permits efficient, DNA-free genome editing in pepper. Remarkably, up to 77.9% of regenerated pepper plants contained heritable edits. This method has been validated with two pepper varieties and is compatible with existing tissue culture protocols.

Targeted mutagenesis in Arabidopsis and medicinal plants using transposon-associated TnpB

Zongyou Lv, Wenhua Chen, Shiyuan Fang, Boran Dong, Xingxing Wang, Lida Zhang, Jingshi Xue, Wansheng Chen

The programmable nuclease TnpB is significantly smaller than Cas9, can edit genes in medicinal plants, includingArtemisia annua,Salvia miltiorrhiza,Scutellaria baicalensis,Isatis indigotica, andCodonopsis pilosula, and has potential uses in molecular breeding to enhance crop yield and quality.

Review Article

Functions and mechanisms of non-histone protein acetylation in plants

Xia Jin, Xiaoshuang Li, Jaime A. Teixeira da Silva, Xuncheng Liu

This review presents an overview of the expanding landscape of the non-histone lysine acetylome across various plant species and highlights the biological functions and regulatory mechanisms of non-histone lysine acetylation in plants.

Mini Review

ProteinS-acylation, a new panacea for plant fitness

Fei Liu, Jin-Yu Lu, Sha Li, Yan Zhang

This review discusses recent progress in understanding the role of proteinS-acylation, a reversible post-translational modification, in receptor signaling, protein targeting, and stress responses to improve our understanding of how plants enhance their fitness under ever-changing and often harsh environmental conditions.

Abiotic Stress Responses

Simultaneous mutations inITPK4andMRP5genes result in a low phytic acid level without compromising salt tolerance in Arabidopsis

Yuying Ren, Mengdan Jiang, Jian-Kang Zhu, Wenkun Zhou, Chunzhao Zhao

Engineering of crops with low phytic acid (InsP6) often impairs other agronomic traits. Simultaneous mutations in the inositol 1,3,4-trisphosphate 5/6-kinase geneITPK4and the ABC transporter geneMRP5result in reduced InsP6 content without affecting plant salt tolerance, providing a promising strategy for breeding crops with low InsP6.

STOP1 regulates CCX1-mediated Ca2+ homeostasis for plant adaptation to Ca2+ deprivation

Wen Hao Tian, Wen Yan Cai, Chun Quan Zhu, Ya Li Kong, Xiao Chuang Cao, Lian Feng Zhu, Jia Yuan Ye, Jun Hua Zhang, Shao Jian Zheng

Calcium ion deficiency induces nuclear accumulation of the transcription factor STOP1, which directly activates the expression ofCATION/CALCIUM EXCHANGER1, thus facilitating calcium efflux from the endoplasmic reticulum to the cytosol to maintain calcium homeostasis in Arabidopsis.

The combination of a microbial and a non-microbial biostimulant increases yield in lettuce (Lactuca sativa) under salt stress conditions by up-regulating cytokinin biosynthesis

Patricia Benito, Marina Celdrán, Javier Bellón, Vicente Arbona, Miguel González-Guzmán, Rosa Porcel, Lynne Yenush, José M. Mulet

The combination of a microbial and a non-microbial biostimulant increased yield of lettuce under salt stress. Application of the non-microbial biostimulant triggered an abscisic acid-dependent response and, when applied with the microbial biostimulant, potentiated the responses triggered by the microbial biostimulant and elicited a cytokinin-dependent response.

Cell and Developmental Biology

A QTLGN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice

Huai-Yu Zhao, Jun-Xiang Shan, Wang-Wei Ye, Nai-Qian Dong, Yi Kan, Yi-Bing Yang, Hong-Xiao Yu, Zi-Qi Lu, Shuang-Qin Guo, Jie-Jie Lei, Ben Liao, Hong-Xuan Lin

In rice, the elite quantitative trait locus alleleGRAIN NUMBER 1.1Bencodes a FLOWERING LOCUS T-LIKE1 protein that improves grain number and yield by affecting polar auxin transport through interaction with the ADP-ribosylation factor-GTPase-activating protein OsZAC.

Functional Omics and Systems Biology

Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation

Wei Tong, Yanli Wang, Fangdong Li, Fei Zhai, Jingjing Su, Didi Wu, Lianghui Yi, Qijuan Gao, Qiong Wu, Enhua Xia

Genomic investigation of 363 diverse tea accessions reveals the fine population structure, genetic diversity, structural variation and dispensable genome architecture of cultivated and wild tea plants as well as the divergent selection signatures ofC. sinensisvar.assamicaandC. sinensisvar.sinensisof cultivated tea plant.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution

Tengfei Liu, Haiyue Liu, Wenfei Xian, Zhi Liu, Yaqin Yuan, Jingwei Fan, Shuaiying Xiang, Xia Yang, Yucheng Liu, Shulin Liu, Min Zhang, Yanting Shen, Yuannian Jiao, Shifeng Cheng, Jeff J. Doyle, Fang Xie, Jiayang Li, Zhixi Tian

A comprehensive phylogenetic analysis revealed that Leguminosae show multiple changes in the flavonoid pathway, including a duplication of the type Ⅱ chalcone isomerase geneCHI; the resulting duplicatedCHI1AandCHI1Bgenes participated in root nodule symbiosis and exhibited structural and functional divergence.

The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis

Junting Feng, Wei Zhang, Chengjie Chen, Yinlong Liang, Tangxiu Li, Ya Wu, Hui Liu, Jing Wu, Wenqiu Lin, Jiawei Li, Yehua He, Junhu He, Aiping Luan

A telomere-to-telomere genome assembly for pineapple integrating germplasm collections, phenotyping, sequencing, and manual inspections with gene structural annotations is provided in the Ananas Genome Database and enabled the identification of high-confidence structural variants and a regulatory gene for red leaves.

Proteomic dynamics revealed sex-biased responses to combined heat-drought stress in Marchantia

Sara Guerrero, Víctor Roces, Lara García-Campa, Luis Valledor, Mónica Meijón

Sex-biased plasticity is crucial for dioecious liverworts to manage terrestrial pressures and adapt to various environments. Examining the effects of combined heat and drought stress inMarchantia polymorphausing a systems biology approach demonstrates how natural variation may have constrained this significant evolutionary step in the plant kingdom.

Molecular Ecology and Evolution

The origin and morphological character evolution of the paleotropical woody bamboos

Jing-Xia Liu, Cen Guo, Peng-Fei Ma, Meng-Yuan Zhou, Ya-Huang Luo, Guang-Fu Zhu, Zu-Chang Xu, Richard I Milne, Maria S. Vorontsova, De-Zhu Li

A robust and time-calibrated phylogeny based on MiddRAD-seq of paleotropical woody bamboos, a distinct hexaploid clade of bamboos with complex evolutionary history and morphology, revealed evolutionary trends in plant habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography.

Photosynthesis and Crop Physiology

Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium,Halorhodospira halochloris

Chen-Hui Qi, Guang-Lei Wang, Fang-Fang Wang, Jie Wang, Xiang-Ping Wang, Mei-Juan Zou, Fei Ma, Michael T. Madigan, Yukihiro Kimura, Zheng-Yu Wang-Otomo, Long-Jiang Yu

Cryo-electron microscopy structural analysis of the light-harvesting-reaction center (LH1–RC) complex from the extremophilic phototrophic purple sulfur bacteriumHalorhodospira halochlorisreveals a structural foundation for LH1’s unique absorbance, the position and function of the carotenoid in the complex, and biochemical adaptations to life in a hot, alkaline, and hypersaline environment.

Plant Biotic Interactions

SERKs serve as co-receptors for SYR1 to trigger systemin-mediated defense responses in tomato

Hyewon Cho, Dain Seo, Minsoo Kim, Bo Eun Nam, Soyoun Ahn, Minju Kang, Geul Bang, Choon-Tak Kwon, Youngsung Joo, Eunkyoo Oh

The peptide hormone systemin induces the association between its receptor, SYSTEMIN RECEPTOR1 and somatic embryogenesis receptor-like kinases (SlSERKs), triggering their mutual trans-phosphorylation and the phosphorylation of the receptor-like cytoplasmic kinase TPK1b, thus promoting defense responses against herbivorous insects in tomato.

Fusarium graminearumeffector FgEC1 targets wheat TaGF14b protein to suppress TaRBOHD-mediated ROS production and promote infection

Shengping Shang, Yuhan He, Qianyong Hu, Ying Fang, Shifeng Cheng, Cui-Jun Zhang

The fungal pathogenFusarium graminearumdelivers the effector FgEC1 into wheat cells, where it indirectly promotes degradation of the reactive oxygen species-producing enzyme TaRBOHD, thus reducing TaRBOHD-mediated reactive oxygen species production, and promoting infection. Overexpression of a target of FgEC1 increased wheat tolerance toF. graminearumwithout reducing yield.