Hybridization can drive speciation. We examine the hypothesis that Castanea henryi var. omeiensis is an evolutionary lineage that originated from hybridization between two near-sympatric diploid taxa, C. henryi var. henryi and C. mollissima. We produce a high-quality genome assembly for mollissima and characterize evolutionary relationships among related chestnut taxa. Our results show that C. henryi var. omeiensis has a mosaic genome but has accumulated divergence in all 12 chromosomes. We observe positive correlation between admixture proportions and recombination rates across the genome. Candidate barrier genomic regions, which isolate var. henryi and mollissima, are re-assorted in the hybrid lineage. We further find that the putative barrier segments concentrate in genomic regions with less recombination, suggesting that interaction between natural selection and recombination shapes the evolution of hybrid genomes during hybrid speciation. This study highlights that reassortment of parental barriers is an important mechanism in generating biodiversity.

Background The importance of psychosocial functioning in the assessment, diagnosis and treatment of major depressive disorder (MDD) is widely recognised. However, there is a lack of effective scales to assess psychosocial functioning in patients with MDD. Aims To develop a professional questionnaire to evaluate the psychosocial functioning of patients with MDD. Methods Using a literature review, an open-ended questionnaire survey, and patient interviews, a theoretical model of psychosocial functioning was constructed, and an initial questionnaire was formed which included four dimensions. After two rounds of testing, using items analysis and exploratory factor analysis, a finalized questionnaire was created. There were 460 patients with MDD selected from six psychiatric hospitals for formal testing using a convenience sampling method. Forty patients were randomly selected and retested one week later to evaluate the test-retest reliability of the scale. The Patient Health Questionnaire-9 (PHQ-9), Short Form of Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q-SF), Sheehan Disability Scale (SDS), and Dysfunctional Attitudes Scale (DAS) provided major standards to check the criterion validity of this questionnaire. Correlation analysis, confirmatory factor analysis, and internal consistency reliability testing were used to examine other psychometric characteristics of the finalized questionnaire. Results The Psychosocial Functioning Questionnaire (PFQ) for patients with MDD included three dimensions: psychological cognitive functioning, subjective well-being, and social functioning, with a total of 18 items. The overall internal consistency reliability of the questionnaire was 0.957, and the test-retest reliability was 0.840. Confirmatory factor analysis showed that the model fitted well: Goodness of Fit Index (GFI)=0.888; Root Mean SquareError of Approximation (RMSEA)=0.085. The total score of PFQ was significantly correlated with the total score of PHQ-9, DAS, SDS and Q-LES-Q-SF (|r|=0.599–0.870, p<0.001). Conclusions The Psychosocial Functioning Questionnaire has good reliability and validity. It can be used to measure the psychosocial functioning of patients with MDD.

Background: Plastid RNA editing is widespread in angiosperms yet remains underexplored in the medicinal non-model species Glycyrrhiza uralensis. This study aimed to (i) comprehensively identify plastid RNA editing sites in G. uralensis, and (ii) compare the detection performance of three library construction strategies: total RNA-seq, rRNA-depleted RNA-seq, and mRNA-seq. Methods: Leaf tissue was used from three wild-sampled individual plants. Plastomes were assembled with GetOrganelle v1.7.0 and annotated using PGA. Strand-specific RNA-seq libraries were mapped to sample-matched plastomes using HISAT2 v2.2.1. Variants were identified using REDItools v2.0 under uniform thresholds. Candidate sites were visually verified in IGV v2.12.3, and read origins were confirmed by BLAST v2.13.0+; artifacts were removed via strand-specific filtering. Results: After stringent filtering, 38 high-confidence RNA editing sites were identified across 19 genes. Total RNA seq performed the best, detecting 37/38 sites consistently, whereas rRNA-depleted libraries detected fewer genuine sites and produced numerous rRNA-linked, noncanonical, noncoding-strand-dominant artifacts. Despite very low rates of plastid mapping, mRNA seq recovered a large fraction of bona fide sites under stringent, strand-aware filtering. Conclusions: We establish a set of 38 high-confidence plastid RNA editing sites in G. uralensis and suggest potential adaptive implications of editing in ndh-related genes. Methodologically, total RNA-seq is recommended for identification using de novo RNA editing due to its high sensitivity and low false-positive rate; publicly available poly(A)-selected mRNA-seq datasets can be repurposed to reliably retrieve plastid RNA editing sites when stringent strand-specific filtering is applied.

Mirabilis himalaica (Nyctaginaceae) is endemic to the Himalayas where it is used in traditional Tibetan folk medicine. In this study, we first presented the complete chloroplast genome of M. himalaica. Complete genome size of M. himalaica ranged from 154,348 to 154,388 bp. The length varied from 85,808 to 85,845 bp in the (large single-copy) LSC region, from 17,935 to 17,938 bp in the (small single-copy) SSC region, and from 25,302 to 25,303 bp in the inverted repeat (IR) region. The overall GC contents of the chloroplast genome sequences were around 36%. Annotation analysis revealed a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis with three M. himalaica samples and five other Nyctaginaceae species showed that Mirabilis including two species was clustered with high bootstrap support. The complete chloroplast genome sequences obtained in this study will provide valuable data for wider studies into the phylogenetics and conservation biology of M. himalaica.

Background: Plastid RNA editing is widespread in angiosperms, yet remains underexplored in the medicinal nonmodel species Glycyrrhiza uralensis. This study aimed to: (i) comprehensively identify plastid RNA editing sites in G. uralensis; and (ii) compare the detection performance of three library construction strategies: total RNA sequencing, rRNA-depleted RNA sequencing, and mRNA sequencing. Methods: Three individuals were resequenced for plastome assembly with GetOrganelle and annotation by PGA. Strandspecific RNAseq libraries were mapped to samplematched plastomes using HISAT2. Variants were called by REDItools2 under uniform thresholds. Candidates were visually verified in IGV and read origins confirmed by BLAST; artefacts were removed via strandspecific filtering. Results: After stringent filtering, 38 high-confidence RNA editing sites were identified across 19 genes. Total RNA seq performed best, detecting 37/38 sites consistently, whereas rRNA depleted libraries detected fewer genuine sites and produced numerous rRNA linked, noncanonical, noncoding strand dominant artefacts. Despite very low plastid mapping, mRNA seq recovered a large fraction of bona fide sites under stringent, strand aware filtering. Conclusions: This study establishes a set of 38 high-confidence plastid RNA editing sites in G. uralensis and reveals the potential adaptive implications of editing in ndh-related genes. Methodologically, total RNA-seq is recommended in de novo RNA editing identification for optimal sensitivity and low false-positive rates, and datasets from mRNA-seq can be reutilized in reliable retrieval of RNA editing sites, provided that stringent strand-specific filtering is applied.