Aug 2026· Scientific Reports· Vol 16· 0 citations· 111 references
Medicine
TL;DR
The PlastidPipeline is developed, which consistently and repeatably provides structurally standardized and annotated, ready-to-analyze plastomes from short-read sequences, and is recommended for the analysis of within-sample read variation, and improved standardization of newly reported plastomes.
Abstract
In phylogeographic studies, genetic distances between individuals are typically small: In the European endemic, declining medicinal plant Arnica montana L., range-wide biogeographic patterns so far remained obscure as sequence diversity in plastome marker regions is very low. While entire chloroplast genomes promise higher resolution, comparing them in great detail is a technical challenge, requiring high accuracy and repeatability in sequencing, assembly and annotation, automated across large sample sets. Using A. montana as our working example, we developed the PlastidPipeline, which consistently and repeatably provides structurally standardized and annotated, ready-to-analyze plastomes from short-read sequences. The PlastidPipeline combines well-tested standard software tools with own scripts, from data cleanup through plastome assembly, structural standardization, annotation, to quality control and raw read backmapping. Using publicly available read data of diverse provenance, we obtained plastid genomes for eight A. montana accessions across Europe, four further species of Arnica and three outgroup species. All A. montana plastomes formed a well-supported clade, split further into an Iberian and a Central/Northern European geographic group, which are, however, connected by patterns of potential heteroplasmy. Beyond demonstrating that pan-plastome phylogeography is both feasible and useful, we recommend the analysis of within-sample read variation, and improved standardization of newly reported plastomes.
The utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae is highlighted, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.
Sadaf Habib, Yong Shi, Jie Zhang et al.· Frontiers in Plant Science· 0 citations
This population-scale plastome dataset provides a practical reference for phylogeographic analysis, marker development, and conservation genomic studies in Cypripedium.
Huiying Shang, Yang Huyan, Yuan Lu et al.· Scientific Data· 0 citations
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.
Yong Shi, Jie-Jun Liu, Lei Ren et al.· Genes· 0 citations
The reliable identification of cultivated and naturalised mulberries is complicated by morphological plasticity, the historical movement of the planting material, and partly discordant nuclear and plastid signals. We evaluated four field-identified Morus alba L. trees, one from each of four localities in Mangystau, Western Kazakhstan, using archived consensus sequences for ITS, matK, rbcL, and trnH-psbA, together with a low-coverage Oxford Nanopore Technologies (ONT) dataset. Because the design comprised one tree per locality (n = 4), analyses were restricted to accession-level descriptive comparisons, and no population-genetic, phylogeographic, or formal phylogenetic inference was attempted. Archived alignment summaries indicated mean pairwise distances of 0.13% for matK, 0.44% for ITS, 0.94% for rbcL, and 2.92% for trnH-psbA; these values are reported as retained dataset descriptors rather than estimates of population diversity. An additional product generated with Rosaceae-derived s6pdh primers was excluded because the target identity and orthology could not be verified. The ONT run yielded 19,958 pass reads (69.27 Mb; read N50 3574 bp). Reference-enriched assembly produced a 14,824 bp candidate plastid-associated contig, approximately 9.3% of a typical Morus plastome. Its short length, incomplete and non-collinear annotations, and the absence of retained depth, polishing, assembly graph, and join support diagnostics preclude its interpretation as a complete, circular, or structurally validated plastome. This study provides a transparent pilot baseline for Mangystau mulberries and establishes quality control criteria for replicated sampling, validated markers, and deeper organelle sequencing.
A. Imanbayeva, N. Duisenova, N. Tolep et al.· International Journal of Pla...· 0 citations
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.
Wei Han, Kai Zhang, Yuanjin Zhao et al.· BMC Plant Biology· 0 citations
Reliable molecular identification of plants depends on reference libraries of DNA sequences, and complete plastid genomes (plastomes) used as super-barcodes are increasingly the reference of choice for taxonomically difficult groups. We assess how ready the flora of Poland is for plastome-based super-barcoding by combining national checklists of vascular plants, mosses, and liverworts with the current availability of complete plastomes in GenBank. For 3339 species we quantify coverage, its distribution across families and genera, the provenance of the sequenced material, and the gap between coverage and expected species-level resolution. A complete plastome was available for 54.4% of species, but coverage was uneven: liverworts (76.0%) and mosses (75.6%) were close to reference-complete, whereas the much larger vascular flora reached only 45.9%. Effective vascular coverage fell to roughly 39% once low-resolution genera were excluded, because many uncovered species belong to apomictic or hybridogenous complexes such as Taraxacum, Hieracium, and Alchemilla, where plastomes alone cannot resolve identity. Most sequenced material was of non-European origin, which weakens fine-scale identification of local populations. We identify 1011 high-value sequencing targets and recommend a tiered, marker-aware strategy combining the plastome with nuclear ribosomal DNA and, selectively, low-copy nuclear or mitochondrial markers. Defining readiness by the proportion of the flora that can actually be identified turns a static inventory into a prioritized roadmap transferable to other Central European floras.
M. Szczecińska, Aniela Garbowska, Natan Pupek et al.· Applied Biosciences· 0 citations