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The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein‐coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16‐trnQ, ycf1, ndhF‐rpl32, petN‐psbM, and rpl32‐trnL, and they may be suitable for the development of robust, authentic, and cost‐effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co‐occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation. Our study provides insight into plastome structure evolution of the genus Blumea and the subfamily Asteroideae (Asteraceae). Previously, the phylogeny of Blumea could not be resolved due to lack of knowledge of suitable polymorphic loci. Based on comparative genomics, we report suitable polymorphic loci which are also co‐occur with repeats and support the role of repeats as proxy for identification of polymorphic loci. The conflicting phylogenetic signals observed at tribe level between plastome and nuclear genome data may be due to reticulate and abrupt evolution which require further investigation. ​

Hibiscus L. (Hibisceae, Malvoideae, Malvaceae) is globally distributed and valued for its ornamental, agricultural, and medicinal significance, yet its taxonomic problems remain unresolved. Here, we de novo assembled 17 complete chloroplast (cp.) genomes representing 16 Hibiscus species, as one species was represented by two varieties, and compared them with 13 previously published genomes of this genus. These genomes ranged from 159,125 to 163,360 base pairs and exhibited a conserved quadripartite structure, encoding 112 unique genes (78 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs). While codon usage, amino acid frequency, substitution patterns, and the expansion and contraction of inverted repeats revealed high similarity, the number of simple sequence repeats (SSRs) varied among species. Comparative analyses identified five non-coding polymorphic loci ( trnH-psbA , ndhF-rpl32 , rps19-rpl22 , trnR-atpA , and ndhD-ccsA ) and six coding loci ( rpl22 , ycf1 , matK , rpl32 , rbcL , and ndhF ) as suitable candidates for DNA barcoding and phylogenetic reconstruction. Phylogenomic analyses based on the cp. genome confirmed the polyphyly of Hibiscus , with Urena Dill. ex L., Malvaviscus Fabr., Kosteletzkya C. Presl, and Kydia Roxb. nested within it. Three major clades were recovered (/Phylloglandula, /Trionum, and /Euhibiscus). Hibiscus volkensii Gürke showed a long branch, suggesting a distinct evolutionary trajectory. Thepparatia scandens (Roxb. ex G.Don) Phuph. appeared as a sister to Hibiscus verdcourtii Craven. Congruence was observed between the cp. genome phylogeny and recent sectional classifications, although Hibiscus sect. Bombicella was confirmed to be polyphyletic. Overall, this study provides insights into the cp. genome evolution of Hibiscus and its implications for the phylogeny of this genus. These findings highlight the need for nuclear genomic data to resolve remaining uncertainties and clarify the taxonomy of this complex genus and other genera within the tribe Hibisceae.

Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.

Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

Assessing the effectiveness of different molecular markers is essential for identification of appropriate ones for crop improvement and conservation, hence, inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers were used for this study. Sixty-six accessions with different genomes obtained from International Transit Center, Belgium, were used for DNA extraction, amplification with ISSR and SCoT markers and agarose gel electrophoresis. The reproducible bands were scored for analyses. We identified high allelic richness of 299 (ISSR) and 326 (SCoT). Polymorphic information contents (ISSR: 0.9225; SCoT: 0.9421) were high but SCoT exhibited higher level of informativeness. The two markers demonstrated high percentage polymorphic loci (ISSR: 91.21–100%; SCoT: 96.97–100%). Other genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon information index were higher in SCoT and further elucidated the usefulness of the markers. Intraspecific genetic diversity, interspecific genetic diversity, coefficient of gene differentiation and level of gene flow revealed extensive gene flow and larger variability within the accessions. Both ISSR and SCoT grouped the accessions via dendrogram, biplot and structure analyses. Though the two marker systems varied in their informativeness, they demonstrated high effectiveness in resolving genetic diversity (GD) of the different accessions, with higher efficiency in SCoT markers. Due to higher GD indices exhibited by SCoT, AS is the most genetically endowed one. Our study showed that SCoT markers are more informative than ISSR for GD exploration, assessment and cluster resolution of Musa species, thereby revealing the potential of SCoT markers for improved breeding and conservation.

Toxoplasma gondii is a protozoan parasite that infects nearly all mammal and bird species worldwide. Usually asymptomatic, toxoplasmosis can be severe and even fatal to many hosts, including people. Elucidating the contribution of genetic variation among parasites to patterns of disease transmission and manifestations has been the goal of many studies. Focusing on the geographic component of this variation, we show that most genotypes are locale-specific, but some are found across continents and are closely related to each other, indicating a recent radiation of a pandemic genotype. Furthermore, we show that the geographic structure of T. gondii is extraordinary in having one population that is found in all continents except South America, whereas other populations are generally confined to South America, and yet another population is found worldwide. Our evidence suggests that South American and Eurasian populations have evolved separately until recently, when ships populated by rats, mice, and cats provided T. gondii with unprecedented migration opportunities, probably during the transatlantic slave trade. Our results explain several enigmatic features of the population structure of T. gondii and demonstrate how pervasive, prompt, and elusive the impact of human globalization is on nature.

Croton L. (Crotonoideae, Euphorbiaceae) is one of the largest angiosperm genera, comprising more than 1100 species with a pantropical distribution; however, the chloroplast (cp) genomes of a few species have been reported. In this study, the complete cp genome of Croton bonplandianus Baill. was newly sequenced, and the cp genome of Croton alabamensis E.A.Sm. ex Chapm. was assembled from publicly available data. These genomes were analyzed together with seven previously published Croton cp genomes to investigate structural variation, inverted repeat (IR) boundary dynamics, and phylogenetic relationships. The nine cp genomes exhibited substantial size variation (150,021–177,025 bp), driven primarily by pronounced differences in IR length (10,100–36,116 bp). Six distinct IR boundary configurations were identified, with IR expansion occurring predominantly at the expense of the large single‐copy (LSC) region rather than the small single‐copy (SSC) region. Phylogenomic analysis based on 78 shared protein‐coding genes supported the monophyly of nine Croton species and placed C. alabamensis and C. bonplandianus as successive early‐diverging lineages among the nine sampled species. Comparative analyses further identified 10 highly polymorphic cp genes as candidate molecular markers for phylogenetic and population‐level studies in the nine species examined, though their utility will require validation before application to additional species. Among the nine studied species, IR contraction and expansion in Croton were largely species‐specific and showed limited phylogenetic conservation. IR boundary shifts at cp genome junctions involved predominantly the LSC region, contrasting with the SSC‐driven patterns commonly reported in other angiosperm lineages; however, broader taxon sampling is needed to determine whether this reflects a genus‐wide pattern or is an artifact of limited sampling. Croton chloroplast genomes exhibit substantial structural diversity driven mainly by asymmetric inverted repeats (IRs) contraction and expansion, despite highly conserved gene content. IR boundary shifts predominantly involved the LSC region, indicating an LSC‐driven evolutionary pattern. The preliminary phylogenomic analyses confirmed the monophyly of Croton and resolved C. alabamensis and C. bonplandianus as early‐diverging lineages. The largely species‐specific IR configurations and the identification of highly polymorphic loci provide a valuable genomic foundation for future systematic, evolutionary, and conservation studies in Euphorbiaceae. However, these results are based on only nine species, and further sampling is needed to draw a final conclusion.

This study aims to evaluate the genetic diversity of the species Robinia pseudoacacia L. using several populations selected from places located in the Crișana Region. The first six ISSRs tested gave distinct bands, with a total of 59 loci, of which 45 were polymorphic (63.85%). The percentage of polymorphic loci varied within populations from 33.33% to 100%. The average number of observed alleles (Na) is 1.7627 and the average effective number of alleles (Ne) is 1.4926, indicating that the effective variability is lower than the observed variability. For the Nei (h) gene diversity index, we recorded an average value of 0.2795, and for allelic entropy, the average value of the Shannon index (I) was 0.4137. The study finds a significant differentiation between populations, with a Gst coefficient value of 0.43 indicating that 43% of the variability is due to interpopulation differences.

In the realm of Aquilaria classification and grading, a persistent market uncertainty persists, questioning whether the basis should be geographical distribution or biological origin. In this study, the effectiveness of matK molecular markers, particularly through eight stable polymorphic loci ( e.g. , +249C for Chinese origin, +435G for Aquilaria sinensis ), emerges as a decisive tool for differentiating Aquilaria species. The integration of matK and trnL-trnF not only validates this efficacy but also streamlines the systematic categorization of 34 agarwood products into four biogeographic pedigrees: Chinese (C1: A. sinensis ; C2: A. malaccensis ), Indonesian ( A. cumingiana ), and Indochinese ( A. rugosa ). Molecular clock analyses trace the genus’s divergence to 6.78 million years ago (Ma) ( A. hirta ), with recent speciation of commercially pivotal species ( A. sinensis :  0.9 Ma; A. malaccensis :  1.0 Ma). Notably, the redefined placement of Gyrinops walla (5.75 Ma) within Aquilaria challenges prior taxonomic assumptions, suggesting revised genus boundaries. The Median-Joining network further visualized these haplotypes, showing key evolutionary transitions, particularly from A. crassna to A. rugosa and A. malaccensis . These findings provide robust tools for species differentiation, insights into evolutionary history, and practical guidance for conservation and trade applications within the field of botany.

Background The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this ‘dark genome’. This goal is complicated by the highly repetitive nature of these sequences in genomes, requiring the deployment of several problem-specific tools as well as the curation of appropriate genome annotations. This pipeline aims to make the analysis of TE sequences and their expression more generally accessible. Results The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs, and is compatible with most eukaryotic species. It implements computational methods tailor-made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent human lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element clades were upregulated in senescence, which included non-reference, intact, and potentially active elements. Conclusions TE-Seq is made available as a Snakemake pipeline which can be obtained at https://github.com/maxfieldk/TE-Seq .