Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits.

Moso bamboo (Phyllostachys edulis), an ecologically and economically important forest species in East Asia, plays vital roles in carbon sequestration and climate change mitigation. However, intensifying climate change threatens moso bamboo survival. Here we generate high-quality haplotype-based pangenome assemblies for 16 representative moso bamboo accessions and integrated these assemblies with 427 previously resequenced accessions. Characterization of the haplotype-based pangenome reveals extensive genetic variation, predominantly between haplotypes rather than within accessions. Many genes with allele-specific expression patterns are implicated in climate responses. Integrating spatiotemporal climate data reveals more than 1050 variations associated with pivotal climate factors, including temperature and precipitation. Climate-associated variations enable the prediction of increased genetic risk across the northern and western regions of China under future emissions scenarios, underscoring the threats posed by rising temperatures. Our integrated haplotype-based pangenome elucidates moso bamboo’s local climate adaptation mechanisms and provides critical genomic resources for addressing intensifying climate pressures on this essential bamboo. More broadly, this study demonstrates the power of long-read sequencing in dissecting adaptive traits in climate-sensitive species, advancing evolutionary knowledge to support conservation.

Background: The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers’ attention. Results: We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans. Conclusions: This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants.

Intercalary meristems (IcMs), specialized developmental zones that drive rapid stem elongation in monocots, exhibit distinct spatiotemporal dynamics; however, their genetic basis remains poorly understood due to their transient activity and cellular heterogeneity. Moso bamboo ( Phyllostachys edulis )—with its exceptional daily growth rates of up to 114.5 cm, prolonged IcM activity spanning 45 to 60 d, and large, accessible culm structure—provides an ideal system for building a comprehensive IcM cell atlas. Here, we integrated a chromosome-level genome assembly of Moso bamboo with a high-resolution anatomical atlas to delineate three critical developmental stages of IcM activity: the initial cell division phase (ID), the rapid cell division phase (RD), and the rapid cell elongation phase (RE). By combining single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics, we reconstructed a dynamic single-nucleus transcriptomic continuum spanning from proliferative to elongation states. Multiomics integration, along with in situ hybridization and ultrastructural imaging, identified IcM cells as short-columnar cells adjacent to elongating ground tissue parenchyma (Gp) cells, with the IcM1 subpopulation functioning as stem-like cells essential for maintaining the proliferative capacity. Pseudotemporal trajectory analysis revealed transcriptional transitions from stem-like IcM states to differentiated Gp cells. Functional experiments revealed that clrGene008562 , a WOX2 homolog, enhances callus regeneration, indicating its potential role in promoting cell division and differentiation processes relevant to IcM development. These findings provide a comprehensive molecular and cellular framework for understanding IcM function and offer valuable multiomics resources for advancing meristem research in bamboo and other Poaceae species.

Bamboo, the fast-growing grass plant, and rattan, the spiky climbing palm, are both essential forest resources that have been closely linked with human lives, livelihoods and material culture since ancient times. To promote genetic and genomic research in bamboo and rattan, a comprehensive and coordinated international project, the Genome Atlas of Bamboo and Rattan (GABR), was launched in 2017. GABR achieved great success during Phase I (2017-2022). We will focus on investigating and protecting bamboo and rattan germplasm resources in Phase II ( 2022-2027). Here, we briefly review the achievements of Phase I and introduce the goals of Phase II.