Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica ‘JinhuaiJ2’, the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.

Background: Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.Methods: In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species,Geodorum eulophioides(endemic and endangered in Southwest China), and a widespread species,G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.Results: The results showed that the nucleotide diversity and heterozygosity ofG. eulophioideswere significantly higher than those ofG. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a fewG. eulophioidesindividuals were detected with genetic components fromG. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat ofG. eulophioidesinvasion byG. densiflorumunder anthropogenic disturbance may be the main factor causing interspecific hybridization.Conclusions: Therefore, reducing or avoiding habitat disturbance is a key measure to protect theG. eulophioidespopulations. This study provides valuable information for future conservation programs for narrowly distributed species.

Cycas (family Cycadaceae), which spread throughout tropical and subtropical regions, is crucial in conservation biology. Due to subtle morphological variations between species, a solid species-level phylogeny for Cycas is lacking. In the present study, we assembled and analyzed the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide diversity. The Cycas chloroplast genome spans from 162,038 to 162,159 bp and contains 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) regions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant variation. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm resources.

Golden Camellia species are highly specific to certain soil environments. Most species are only native to calcareous soils in karst regions, except for a few that grow only in acidic soils. Our aim is to elucidate the adaptation mechanisms of the species of calcareous-soil golden Camellia (CSC) and acidic-soil golden Camellia (ASC) to habitat soils through plant–soil nutrient characteristics and their relationships. We investigated 30 indices for soils and plants. Compared with ASC, CSC had more fertile soil, while their plant tissues exhibited stronger Ca, P, and Mn and weaker K storage, which may be important mechanisms for adapting to habitat soils. However, ASC showed a higher biological absorption coefficient (BAC) for nutrients, which may contribute to the adaptation of ASC to relatively barren acidic soils. Both CSC and ASC showed much higher BAC and accumulation of Ca than other nutrients. We also found that the concentrations of nutrients in the different tissues varied considerably between species. Correlation analysis revealed 135 significant relationships between the 30 indices, with the soil pH and soil Ca levels being the most important factors influencing the nutrient uptake network. This information helps in understanding the adaptation mechanisms of karst plants to habitat soils.

The genus Ormosia comprises approximately 130 species, which are found in tropical regions all over the world. The taxonomy and evolutionary history are still ambiguous due to the lack of a solid phylogeny at the species level. Due to the fast advancement of high-throughput sequencing technology, it is now possible to retrieve the full chloroplast (cp) genome sequence, providing a molecular basis for phylogenetic analysis. Five species of Ormosia were used in this work, and their whole cp genomes were sequenced. One circular, quadripartite-structured molecule, ranging from 169,797 to 173,946 base pairs in length, was present in all five Ormosia species. The cp genomes of the five newly sequenced Ormosia species were further compared with the published cp genomes of O. pinnata. Ten hypervariable regions (Pi > 0.025) were uncovered in the Ormosia chloroplast genomes, among which petN-psbM showed the highest Pi value. Phylogenetic analysis revealed that O. microphylla and O. olivacea clustered with strong support. O. balansae was resolved as a sister to O. pinnata, and they were further found to be sisters to the remaining 13 Ormosia species. The cp genes of O. elliptica showed a close relationship to O. hosiei, and O. semicastrata clustered with O. emarginata. Taken together, the comprehensive analysis of the complete cp genomes of five Ormosia species offers valuable insight and information for reconstructing their phylogeny and sheds light on the evolutionary dynamics of the chloroplast genome in Ormosia.