ArticleGigaScience2025
Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- A chromosome-scale genome assembly of Tigridiopalma magnifica.Scientific data · 2026Article
- Chromosome-Level Genome Assembly ofPlants (Basel, Switzerland) · 2026Article
- A chromosome-scale assembly of Ormosia boluoensis (Fabaceae).Scientific data · 2025Article
- Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.GigaScience · 2025Article
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7 authors.
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Abstract
backgroundThe genus Ormosia belongs to the Fabaceae family; almost all Ormosia species are endemic to China, which is considered one of the centers of this genus. Thus, genomic studies on the genus are needed to better understand species evolution and ensure the conservation and utilization of these species. We performed a chromosome-scale assembly of O. purpureiflora and updated the chromosome-scale assemblies of O. emarginata and O. semicastrata for comparative genomics.
findingsThe genome assembly sizes of the 3 species ranged from 1.42 to 1.58 Gb, with O. purpureiflora being the largest. Repetitive sequences accounted for 74.0-76.3% of the genomes, and the predicted gene counts ranged from 50,517 to 55,061. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis indicated 97.0-98.4% genome completeness, whereas the long terminal repeat (LTR) assembly index values ranged from 13.66 to 17.56, meeting the "reference genome" quality standard. Gene completeness, assessed using BUSCO and OMArk, ranged from 95.1% to 96.3% and from 97.1% to 98.1%, respectively.Characterizing genome architectures further revealed that inversions were the main structural rearrangements in Ormosia. In numbers, density distributions of repetitive elements revealed the types of Helitron and terminal inverted repeat (TIR) elements and the types of Gypsy and unknown LTR retrotransposons (LTR-RTs) concentrated in different regions on the chromosomes, whereas Copia LTR-RTs were generally evenly distributed along the chromosomes in Ormosia.Compared with the sister species Lupinus albus, Ormosia species had lower numbers and percentages of resistance (R) genes and transcription factor genes. Genes related to alkaloid, terpene, and flavonoid biosynthesis were found to be duplicated through tandem or proximal duplications. Notably, some genes associated with growth and defense were absent in O. purpureiflora.By resequencing 153 genotypes (∼30 Gb of data per sample) from 6 O. purpureiflora (sub)populations, we identified 40,146 single nucleotide polymorphisms. Corresponding to its very small populations, O. purpureiflora exhibited low genetic diversity.
conclusionsThe Ormosia genome assemblies provide valuable resources for studying the evolution, conservation, and potential utility of both Ormosia and Fabaceae species.
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