“Cuohu Bazi” (CHBZ) is an ancient sorghum variety collected from the fields of China, known for its agronomic traits like dwarf stature, early maturation. In this study, we present the first telomere-to-telomere (T2T) and gap-free genome assembly of CHBZ using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. The assembled genome comprises 724.85 Mb, effectively resolving all 3,913 gaps that were present in the previous sorghum BTx623 reference genome. Notably, the T2T assembly captures 10 centromeres and all 20 telomeres, providing strong support for their integrity. This assembly is of high quality in terms of contiguity (contig N50: 71.1 Mb), completeness (BUSCO score: 99.01%, k-mer completeness: 98.88%), and correctness (QV: 61.60). Repetitive sequences accounted for 70.41% of the genome and a total of 32,855 protein-coding genes have been annotated. Furthermore, 161 CHBZ-specific presence/absence variants genes have been identified when comparing to BTx623 genome. This study provides valuable insights for future research on sorghum genetics, genomics, and evolutionary history.

Background: Common bean is a significant grain legume in human diets. However, the lack of a complete reference genome for common beans has hindered efforts to improve agronomic cultivars. Findings: Herein, we present the first telomere-to-telomere (T2T) genome assembly of common bean (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The assembly resulted in a genome size of 560.30 Mb with an N50 of 55.11 Mb, exhibiting high completeness and accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). The sequences were anchored into 11 chromosomes, with 20 of 22 telomeres identified, leading to the formation of 9 T2T pseudomolecules. Furthermore, we identified repetitive elements accounting for 61.20% of the genome and predicted 29,925 protein-coding genes. Phylogenetic analysis suggested an estimated divergence time of approximately 11.6 million years ago between P. vulgaris and Vigna angularis. Comparative genome analysis revealed the expanded gene families and variations between YP4 and G19833 associated with defense response. Conclusions: The T2T reference genome and genomic insights presented here are crucial for future genetic studies not only in common bean but also in other legumes.

Broomcorn millet (Panicum miliaceum L.), known for its traits of drought resistance, adaptability to poor soil, short growth period, and high photosynthetic efficiency as a C₄ plant, represents one of the earliest domesticated crops globally. This study reports the telomere-to-telomere (T2T) gap-free reference genome for broomcorn millet (AJ8) using PacBio high-fidelity (HiFi) long reads, Oxford Nanopore long-read technologies and high-throughput chromosome conformation capture (Hi-C) sequencing data. The size of AJ8 genome was approximately 834.7 Mb, anchored onto 18 pseudo-chromosomes. Notably, 18 centromeres and 36 telomeres were obtained. The assembled genome showed high quality in terms of completeness (BUSCO score: 99.6%, QV: 61.7, LAI value: 20.4). In addition, 63,678 protein-coding genes and 433.8 Mb (~52.0%) repetitive sequences were identified. The complete reference genome for broomcorn millet provides a valuable resource for genetic studies and breeding of this important cereal crop.

Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the TaCRY gene family was performed in wheat, identifying 12 TaCRY members localized to distinct chromosomes 2, 6, and 7. TaCRYs contain the conserved PHR and CCT domains and diverse gene structures. Collinearity relationships indicated their dynamic evolution patterns during polyploidization. Cis-acting elements of TaCRY members associated with light responsiveness, phytohormone signaling, and abiotic stress were also identified. Transcriptome analysis revealed that the differential expression patterns of TaCRY members under seed vigor process. This study expands our understanding of TaCRY diversity and provides valuable molecular information for marker-assisted selection in wheat improvement.

The MYB-CC gene family is implicated in the response to phosphate deficiency in rice, wheat, and soybean. We aimed to identify the MYB-CC gene family members and predict their function in sorghum (Sorghum bicolor (L.) Moench). A systemic genome-wide analysis of the MYB-CC gene family in sorghum was performed. The mRNA expression level of SbMYB-CC genes in root tissue under low phosphate condition was detected by using qRT-PCR. A total of 17 SbMYB-CC genes were identified in the sorghum genome. Phylogenetic analysis revealed that SbMYB-CC proteins could be classified into five groups. Promoter regions in SbMYB-CC genes contained multiple cis-acting elements related to light response, hormone regulation, and stress response. Phylogenetic and collinearity analyses revealed MYB-CC proteins to be conserved among sorghum, rice, and maize; the SbMYB-CC gene family experienced strong purifying selection during evolution. Based on the transcriptome data, results revealed that SbMYB-CC genes presented different expression patterns in each tissue and these genes had obvious spatiotemporal expression characteristics. QRT-PCR assays showed that the expression level of SbMYB-CC1 was significantly increased under low phosphorus stress; the mRNA expression level of SbMYB-CC3, SbMYB-CC4, SbMYB-CC10, SbMYB-CC11, and SbMYB-CC16 were significantly decreased (P < 0.05). Genome-wide identification of the SbMYB-CC genes revealed the characterization and potential biological functions of this gene family in sorghum. This study also provides valuable information for further research on candidate SbMYB-CC genes in response to phosphate deficiency in sorghum.