Comparative plastome analysis and plastomic phylogeny of Moraceae with expanded species-level sampling.

Comparative plastid genomics of five Ormosia species (fabaceae): insights into structural variation and morphological homoplasy

Comparative plastome analyses of Lewinskya (Orthotrichaceae): insights into genome structure, molecular evolution, and phylogenetic relationships.

The newly assembled Lewinskya plastomes expand genomic resources for Orthotrichaceae and show that chloroplast genome evolution in the sampled species is structurally conservative but contains informative localized variation.

Comparative plastome analysis and phylogenetic relationships of Chinese Myricaria species (Tamaricaceae)

The genus Myricaria (Tamaricaceae) comprises shrubs widely distributed across arid and high-altitude regions of Eurasia, with China representing an important diversity center, particularly in the Qinghai–Tibetan Plateau and adjacent areas. To investigate plastome evolution and phylogenetic relationships within this genus, we sequenced and comparatively analyzed complete plastomes of five Myricaria species from China, together with those of Reaumuria as an outgroup. All plastomes exhibited a typical quadripartite structure and highly conserved gene composition, containing 127–135 genes, indicating strong structural stability across the genus. Despite the overall conservation of plastome architecture, minor size differences were observed and were mainly associated with contraction and expansion of inverted repeat (IR) boundaries. Comparative analyses revealed heterogeneous patterns of sequence divergence, with nucleotide variation primarily concentrated in intergenic regions and a limited number of protein-coding genes, whereas IR regions showed relatively high conservation. Simple sequence repeats (SSRs) and long repeats displayed species-specific distribution patterns, contributing to localized plastome variation. Sliding window analysis identified several mutation hotspots mainly located in single-copy regions, suggesting their potential utility for species identification and phylogenetic studies. Phylogenomic analyses based on complete plastome sequences strongly supported the monophyly of Myricaria and resolved major relationships among sampled species. However, limited resolution among some closely related taxa suggests recent diversification and possible incomplete lineage sorting. Overall, Myricaria plastomes show a pattern of highly conserved genome structure coupled with localized sequence divergence, providing valuable resources for phylogenetic resolution, species identification, and plastome evolutionary studies.

Plastome evolution and phylogenomic insights from representative taxa across all nine subfamilies of Malvaceae.

Malvaceae Juss. comprises nine subfamilies and approximately 4,225 species, many of which are ecologically significant and several of which are cultivated for their high economic value. However, the backbone phylogeny of the family remains poorly resolved, and comprehensive structural variations across the entire family's plastomes are not comprehensively investigated. We newly sequenced 45 Malvaceae samples and integrated them with 85 plastomes from GenBank for phylogenetic analyses. After excluding two outgroups and four plastomes containing gaps, 124 Malvaceae plastomes were used for comparative structural analyses. The newly assembled plastomes exhibit a typical quadripartite structure, with length ranging from 158,346 to 163,741 bp and encoding 129-132 genes. We identified five distinct types of boundaries between inverted repeat regions (IRs) and single-copy (SC) regions. Furthermore, six coding genes (e.g., matK, ndhF) and 14 non-coding regions (e.g., trnH-psbA) were identified as highly variable, providing potential DNA markers for species delimitation. Analyses of simple sequence repeats (SSRs) and long repeats revealed unique repeat patterns in Durio Adans., while codon usage bias analysis revealed a strong A/T preference across this family. Selection pressure analysis detected positive selection (dN/dS > 1) in the rpl23 gene, suggesting its potential role in adaptive evolution. Phylogenomic analyses reconstructed a highly supported backbone topology, resolving Malvaceae into two major clades: Byttneriina and Malvadendrina. Within Malvadendrina, Helicteroideae was the earliest-diverging lineage, and Tilioideae was strongly supported as sister to Dombeyoideae. Additionally, Hibiscus L. and Sida L. were confirmed to be non-monophyletic. This study clarifies the major phylogenetic relationships within Malvaceae using a densely sampled plastome dataset and provides novel insights into the structural features and evolution of Malvaceae plastomes.

The Complete Chloroplast Genome of Ficus gasparriniana var. laceratifolia Reveals Discordance Between Morphology-Based Classification and Plastid Phylogeny

This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement in F. gasparriniana, providing a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.

Comparative plastome analyses and phylogenetic insights of Stellaria (Caryophyllaceae)

Stellaria (Caryophyllaceae) comprises approximately 112 species globally, with China serving as a significant center of diversity hosting about 64 species. Despite its taxonomic importance, the genus remains insufficiently studied in China. Previous phylogenetic studies relying on limited DNA barcodes produced weakly supported inferences, while those based on chloroplast genomes are currently lacking. Here, we characterize the chloroplast genome structure and reconstruct its highly resolved infrageneric phylogeny using 60 newly sequenced plastomes. All plastomes displayed a conserved quadripartite structure, with lengths varying from 147,205 bp to 149,409 bp, GC contents ranging from 36.6% to 36.7%, and gene counts spanning 128 to 129 genes. Codon usage patterns were highly conserved with leucine encoded by UUA exhibiting the highest relative synonymous codon usage. A total of 55–74 simple sequence repeats and 42–64 long repeats were detected. Three hypervariable regions—petN-psbM, trnP-rpl33, and ycf1 were identified as promising candidate DNA barcodes. Phylogenomic analysis resolved Stellaria into three strongly supported major clades and 15 well-defined subclades. The results are largely consistent with the established phylogeny of Stellaria. However, we observed certain discrepancies within specific clades. We propose some suggestions for these clades and species based on morphological and molecular evidence. This study provides the first comprehensive phylogenetic framework for Stellaria based on the chloroplast genome, establishing a robust foundation for future taxonomic revisions and evolutionary studies.