The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast

The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae

MAIN CONCLUSION

We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.

Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world's top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy and phylogenetic relationships of Impatiens species are still controversial. In order to better understand their chloroplast properties and phylogenetic evolution, nine Impatiens plants (Impatiens repens, Impatiens rectirostrata, Impatiens baishaensis, Impatiens rostellata, Impatiens faberi, Impatiens oxyanthera, Impatiens tienchuanensis, Impatiens blepharosepala, Impatiens distracta) were sequenced, and their complete chloroplast genomes were analysed. Nine species of Impatiens chloroplast genomes ranged in length from 150,810 bp (I. rectirostrata) to 152,345 bp (I. blepharosepala). The chloroplast genomes were all typical circular DNA molecules, and the GC content in each region was consistent with the published chloroplast genomes of Impatiens plants. The results showed that the seven mutational hotspots (trnL-UAG, ndhG, ycf1, ccsA, rrn23, trnA-UGC, and ycf2) could be used as supporting data for further analyses of the phylogenetic tree and species identification. In addition, the results of the phylogenetic tree support that Balsaminaceae is a monophyletic taxon, and that Hydrocera triflora is at the base of the branch, is the original species of Balsaminaceae, and is in a sister group relationship with Impatiens species. The results of this paper enrich the data of Impatiens chloroplast genomes, and the availability of these chloroplast genomes will provide rich genetic information for species identification, thus enhancing the taxonomic accuracy and phylogenetic resolution of Impatiens, and further promoting the investigation and rational use of Impatiens plant resources.

The complete plastid genome of Abrus pulchellus subsp. mollis (Leguminosae): a medicinal plant in Southern China

The subspecies Abrus pulchellus subsp. mollis exhibits pharmacological properties akin to the traditional Chinese medicinal plant Abri Herba (A. pulchellus subsp. cantoniensis (Hance) Verdc.). In this report, we unveil the plastid genome of A. pulchellus subsp. mollis. The genome spans 156,322 base pairs (bp), comprising a large single-copy (LSC) region of 86,633 bp, a small single-copy (SSC) region of 18,219 bp, and two distinct inverted repeat regions (IRs) of 25,735 bp each. Annotation process cataloged a total of 111 genes within this genome, including 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The overall guanine-cytosine (GC) content of the plastome is 35.5%. Phylogenetic analysis utilizing maximum-likelihood (ML) based on 16 complete plastid genomes reveals a close clustering of three Abrus taxa, namely A. pulchellus subsp. mollis, A. pulchellus subsp. cantoniensis, and A. precatorius. Notably, A. pulchellus subsp. cantoniensis clusters with A. precatorius as a sister group, distinct from A. pulchellus subsp. mollis. These findings highlight significant differences between the plastid genomes of the two subspecies, laying the foundation for future research on the identification of medicinal herbs and germplasm resources related to these subspecies.

Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris

Lens lamottei is a member of the Fabaceae family and the second gene pool of the genus Lens. The environmental factors that drove the divergence among wild and cultivated species have been studied extensively. Recent research has focused on genomic signatures associated with various phenotypes with the acceleration of next-generation techniques in molecular profiling. Therefore, in this study, we provide the complete sequence of the chloroplast genome sequence in the wild Lens species L. lamottei with a deep coverage of 713 × next-generation sequencing (NGS) data for the first time. Compared to the cultivated species, Lens culinaris, we identified synonymous, and nonsynonymous changes in the protein-coding regions of the genes ndhB, ndhF, ndhH, petA, rpoA, rpoC2, rps3, and ycf2 in L. lamottei. Phylogenetic analysis of chloroplast genomes of various plants under Leguminosae revealed that L. lamottei and L. culinaris are closest to one another than to other species. The complete chloroplast genome of L. lamottei also allowed us to reanalyze previously published transcriptomic data, which showed high levels of gene expression for ATP-synthase, rubisco, and photosystem genes. Overall, this study provides a deeper insight into the diversity of Lens species and the agricultural importance of these plants through their chloroplast genomes.

Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe²⁺ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.