A telomere-to-telomere genome of raintree (Samanea Saman) reveals its ecological adaptation characteristics of nyctinastic movement and symbiotic nitrogen fixation

Raintrees are the predominant species within tropical monsoon forest ecosystems, largely due to their distinctive ecological adaptations, such as nyctinastic movement and nitrogen fixation. However, the comprehensive understanding of their functions has been constrained by lack of genomic resources. Here, we present the first T2T genome of the raintree, comprising 13 pseudo-chromosomes and a contig N50 42.86 Mb, with 25,997 gene models annotated. Additionally, we sequenced the genome of the rhizobium symbiotic with the raintree, measuring 7.28 Mb and containing 6,882 annotated genes, and designated it as Bradyrhizobium saman. Through transcriptomic analysis, we identified 41 key genes that are significantly upregulated in pulvinus cells, which are exclusively involved in nyctinastic movement. These genes include basic regulatory factors, ion transporters, and aquaporins. Meanwhile, RNA-seq identified 699 core genes upregulated in root nodules, crucial for symbiotic nitrogen fixation. These include seven SsaHGs coding hemoglobin proteins that extremely high expressed to maintain anaerobic conditions in symbiosomes; 26 genes for amino acid transporters, glutamate synthetases (SsaGh) and aspartate synthetases (SsaAsn), 16 for auxin transport facilitators, and nine in cytokinin signaling. Furthermore, 17 MYB transcription factors are upregulated. These genomic resources and findings are vital for enhancing raintree genetics and investigating their ecological adaptations.