Camellia meiocarpa Hu, a member of Youcha species in the genus Camellia, is an important woody edible Youcha plant with high ecological and economic value. The haplotype-resolved genome assembly of this tetraploid species can shed light on genomic evolution and the functional divergence among subgenomes and haplotypes. In this study, we achieved the first chromosome-level haplotype-resolved genome assembly using PacBio HiFi, Hi-C, and Illumina sequencing. The scaffolds, with an N50 of 44.46 Mb and 41.40 Mb, were mapped to 60 chromosomes and four distinct haplotypes, each with unique transposon features. The haplotypes varied in length (2967.25 Mb to 3041.66 Mb) and contained 51,336 to 52,631 protein-coding genes, 99.4% of which were annotated. Non-coding RNAs and repetitive elements were identified across haplotypes. This comprehensive genomic resource will enhance molecular and genetic studies, aiding in the conservation and utilization of Youcha.

Coffea arabica L. var. ‘Kona Typica’ is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of ‘Kona Typica’ using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of ‘Kona Typica’ provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

C₄ photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C₄ photosynthesis appears to contradict the complex anatomical and biochemical modifications required for the transition from C₃ to C₄ photosynthesis. In this study, we conducted an integrated analysis of genomics and transcriptomics to elucidate the molecular underpinnings of convergent C₄ evolution in the grass family. Our genome-wide exploration of C₄-related gene families suggests that the expansion of these gene families may have played an important role in facilitating C₄ evolution in the grass family. A phylogenomic synteny network analysis uncovered the emergence of C₄ genes in various C₄ grass lineages from a common ancestral gene pool. Moreover, through a comparison between non-C₄ and C₄ PEPCs, we pinpointed 14 amino acid sites exhibiting parallel adaptations. These adaptations, occurring post the BEP–PACMAD divergence, shed light on why all C₄ origins in grasses are confined to the PACMAD clade. Furthermore, our study revealed that the ancestor of Chloridoideae grasses possessed a more favorable molecular preadaptation for C₄ functions compared to the ancestor of Panicoideae grasses. This molecular preadaptation potentially explains why C₄ photosynthesis evolved earlier in Chloridoideae than in Panicoideae and why the C₃-to-C₄ transition occurred once in Chloridoideae but multiple times in Panicoideae. Additionally, we found that C₄ genes share similar cis-elements across independent C₄ lineages. Notably, NAD-ME subtype grasses may have retained the ancestral regulatory machinery of the C₄ NADP-ME gene, while NADP-ME subtype grasses might have undergone unique cis-element modifications.

Anthurium amnicola is in the monocot family Araceae, subfamily Pothoideae and is a contributing species in Hawaii floriculture industry hybrids. To support future genetic improvements to this commodity, we sequenced and assembled the A. amnicola genome to chromosome-scale using PacBio HiFi and short-read Hi-C sequencing. A total of 98.51% of the 4.79 Gb genome is anchored into 15 chromosomes, with 99.2% gene completeness and a high LTR assembly index (LAI) score of 21.73, indicative of a complete, high-quality assembly. Annotation reveals the presence of 20,380 protein-coding genes, with 78.52% of the genome composed of repetitive sequences, predominantly long terminal repeat retrotransposons (LTR-RT). Phylogenetic analysis identified evolutionary relationships between A. amnicola and representative species in the Araceae and other plant families. This study provides the first reference genome sequence for the neotropical genus Anthurium and insights into Araceae evolution, benefiting the floriculture industry and evolutionary studies.

Lablab purpureus (L.) Sweet, a resilient tropical legume critical for sustainable agriculture, is prized for its adaptability, nutritional richness, and drought tolerance. Here, we present the first telomere-to-telomere (T2T) genome assembly of Lablab purpureus (L.) cv. Linghu integrating PacBio HiFi sequencing, ultra-long Oxford Nanopore Technologies (ONT) reads, and Hi-C scaffolding. The complete assembly spanning 460.76 Mb with contig N50 of 40.3 Mb resolved all the gaps, telomeres, and centromeres across the 11 chromosomes. We annotated 29,280 protein-coding genes, with functional roles assigned to 90.3% of genes. Repetitive elements constitute 38.38% of the genome, dominated by long terminal repeat retrotransposons (31.14%). Crucially, we resolved all centromeres (1.42–6.97 Mb) and telomeres, addressing pervasive gaps and mis-assemblies in prior assemblies. Rigorous validation using Merqury, CRAQ, and BUSCO confirmed exceptional assembly accuracy and continuity. This T2T genome provides an unparalleled resource for functional genomics in L. purpureus, enabling precise exploration of stress adaptation, nutrient biosynthesis, and yield-related traits. It further establishes a gold-standard reference for comparative legume genomics and molecular breeding in understudied crops.