Search Results (31)

Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, there is a notable lack of research on its mitogenomes. We utilized PMAT to assemble the mitogenomes of six Rubus species according to long-read HiFi reads and annotated them through homologous alignment. Subsequently, we compared their characteristic differences within Rubus mitogenomes. The complete mitogenomes of R. parviflorus, R. spectabilis, R. idaeus, R. armeniacus, and R. caesius all exhibit master circle structures, with lengths ranging from 360,869 bp to 447,754 bp. However, R. chamaemorus displays a double-circle structure composed of two small circular molecules, spanning 392,134 bp. These mitogenomes encode a total of 54–61 genes, including 33–34 PCGs, 17–24 tRNAs, and 3 rRNA genes. Compared to the other five Rubus species, R. chamaemorus has fewer sequence repeats. These six species exhibit similar codon usage patterns. A large number of gene transfers were detected between organellar genomes of six Rubus species. Additionally, two phylogenetic trees were constructed using 31 mitogenomes and 94 chloroplast genomes, revealing a minor conflict within Rubus. Overall, this study clarifies the mitogenome characteristics of Rubus and provides valuable insights into the evolution of the genus. Full article

Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as “La Mei” in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (−0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T’s and G’s in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution. Full article

The phenomenon of heterochrony, or shifts in the relative timing of ontogenetic events, is important for understanding many aspects of plant evolution, including applied issues such as crop yield. In this paper, we review heterochronic shifts in the evolution of an important floral organ, the carpel. The carpels, being ovule-bearing organs, facilitate fertilisation, seed, and fruit formation. It is the carpel that provides the key character of flowering plants, angiospermy. In many angiosperms, a carpel has two zones: proximal ascidiate and distal plicate. When carpels are free (apocarpous gynoecium), the plicate zone has a ventral slit where carpel margins meet and fuse during ontogeny; the ascidiate zone is sac-like from inception and has no ventral slit. When carpels are united in a syncarpous gynoecium, a synascidiate zone has as many locules as carpels, whereas a symplicate zone is unilocular, at least early in ontogeny. In ontogeny, either the (syn)ascidiate or (sym)plicate zone is first to initiate. The two developmental patterns are called early and late peltation, respectively. In extreme cases, either the (sym)plicate or (syn)ascidiate zone is completely lacking. Here, we discuss the diversity of carpel structure and development in a well-defined clade of angiosperms, the monocotyledons. We conclude that the common ancestor of monocots had carpels with both zones and late peltation. This result was found irrespective of the use of the plastid or nuclear phylogeny. Early peltation generally correlates with ovules belonging to the (syn)ascidiate zone, whereas late peltation is found mostly in monocots with a fertile (sym)plicate zone. Full article

Fe-S clusters are essential cofactors for the activity of a large variety of metalloproteins that play important roles in respiration, photosynthesis, nitrogen fixation, regulation of gene expression, and numerous metabolic pathways, including biosynthesis of other protein cofactors. Assembly of iron and sulfur atoms into a cluster, followed by its insertion into the polypeptide chain, is a complex process ensured by multiproteic systems. Through evolution, eukaryotes have acquired two Fe-S protein biogenesis systems by endosymbiosis from bacteria. These systems, ISC and SUF, are compartmentalized in mitochondria and plastids, respectively. The eukaryotic Fe-S protein biogenesis system (CIA) is dedicated to the biogenesis of cytosolic and nuclear Fe-S proteins. While the CIA system is absent in bacteria, at least two of its components share homologies with bacterial Fe-S protein biogenesis factors, Mrp and SufT. Here, we provide an overview of the role of Mrp and SufT in Fe-S protein biogenesis in bacteria, aiming to put forward specific but also common features with their eukaryotic CIA counterparts. Full article

Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes. Full article

Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns. Full article

Bromus picoeuropeanus is a recently described species belonging to a complex genus of grasses. It inhabits stony soils at heights ranging from 1600 to 2200 m in Picos de Europa (Cantabrian Mountains, northern Spain). This species is morphologically very similar to B. erectus, partially sharing its presumed distribution range. We aim to determine the relationship between these species and their altitudinal ranges in Picos de Europa and the Cantabrian Mountains by conducting phylogenetic analyses based on nuclear (ETS and ITS) and chloroplastic (trnL) markers. Phylogenetic trees were inferred by Maximum Likelihood and Bayesian Inference. Haplotype networks were estimated based on the plastid marker. Although the ITS topologies could not generate exclusive clades for these species, the ETS analyses generated highly supported B. picoeuropeanus exclusive clades, which included locations outside its altitudinal putative range. The ETS-ITS and ETS-ITS-trnL topologies generated B. picoeuropeanus exclusive clades, whereas the trnL-based trees and haplotype networks were unable to discriminate B. erectus and B. picoeuropeanus. This evidence suggests that B. picoeuropeanus is a separate species with a larger distribution than previously thought, opening new questions regarding the evolution of B. erectus and other similar species in European mountainous systems. However, more information is needed regarding B. picoeuropeanus susceptibility to temperature rises. Full article

Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives. Full article

Salicornia is a highly taxonomically problematic genus due to the reduced morphological observable characters. Ten Eurasian species are currently recognized: S. alpini, S. europaea, S. fruticosa, S. hispanica, S. lagascae, S. perennans, S. perennis, S. persica, S. procumbens, and S. pruinosa. In addition, eleven subspecies are accepted, mainly based on their distribution areas. Along the Venetian coasts and in Sardinia, in the past, an endemic species called S. veneta was recognized, but this name was later synonymized with S. procumbens subsp. procumbens. The aim of the present research is investigating different Italian Salicornia populations by a molecular point of view, using the nuclear ribosomal external transcribed spacer ETS and the plastid psbA-trnH intergenic spacer. A particular focus is on the comparison between Venetian (including those occurring in locus classicus of S. veneta) and Sardinian S. procumbens and other Italian populations of this species. The molecular analyses based on the plastid marker highlight that the Italian S. procumbens populations form two well distinct groups. In particular, some of the Venetian (Locus classicus of S. veneta) and all the Sardinian specimens are genetically distinct (=plastid haplotype 1) from the other investigated populations (=plastid haplotype 2). This indicates that the psbA-trnH haplotype 1 glassworts represent a distinct entity, which we suppose to coincide with the former S. veneta. Therefore, we suggest to recognize this taxonomic entity at the subspecies rank, as S. procumbens subsp. veneta comb. and stat. nov. However, contrary to the results found with the plastid psbA-trnH intergenic spacer, the ETS locus does not show a separation into two distinct clades for S. procumbens, probably due to a different evolution of the two loci. Nevertheless, in the ETS phylogenetic reconstruction, the Sardinian specimens (=ribotypes 2 and 3) are placed, together with a Moroccan sample, in a subclade separated from all the other S. procumbens. These results suggest that the Sardinian populations can represent a subspecies/incipient speciation process, probably due to geographic isolation. In the light of this, morphometric analyses (k-means, MANOVA, PCA, DA, and Box-Plot) have been carried out on the Sardinian and Venetian populations to verify if this distinction is detectable also by a morphological point of view. The morphometric analyses highlight the existence of two groups, concerning both the nuclear and plastid trees. Six characters were found to be diagnostic. Full article

Kitagawia Pimenov is one of the segregate genera of Peucedanum sensu lato within the Apiaceae. The phylogenetic position and morphological delimitation of Kitagawia have been controversial. In this study, we used plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences to reconstruct the phylogeny of Kitagawia, along with comparative plastome and morphological analyses between Kitagawia and related taxa. The phylogenetic results identified that all examined Kitagawia species were divided into Subclade I and Subclade II within the tribe Selineae, and they were all distant from the representative members of Peucedanum sensu stricto. The plastomes of Kitagawia and related taxa showed visible differences in the LSC/IRa junction (JLA) and several hypervariable regions, which separated Subclade I and Subclade II from other taxa. Fruit anatomical and micromorphological characteristics, as well as general morphological characteristics, distinguished the four Kitagawia species within Subclade I from Subclade II and other related genera. This study supported the separation of Kitagawia from Peucedanum sensu lato, confirmed that Kitagawia belongs to Selineae, and two species (K. praeruptora and K. formosana) within Subclade II should be placed in a new genus. We believe that the “core” Kitagawia should be limited to Subclade I, and this genus can be distinguished by the association of a series of morphological characteristics. Overall, our study provides new insights into the phylogeny, plastome evolution, and taxonomy of Kitagawia. Full article

DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species. Full article

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species. Full article

Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal ‘V. tricolor species complex’: V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium. Full article

Polyploidy is a widespread phenomenon across angiosperms, and one of the main drivers of diversification. Whilst it frequently involves hybridisation, autopolyploidy is also an important feature of plant evolution. Minority cytotypes are frequently overlooked due to their lower frequency in populations, but the development of techniques such as flow cytometry, which enable the rapid screening of cytotype diversity across large numbers of individuals, is now providing a more comprehensive understanding of cytotype diversity within species. Senecio doronicum is a relatively common daisy found throughout European mountain grasslands from subalpine to almost nival elevations. We have carried out a population-level cytotype screening of 500 individuals from Tête Grosse (Alpes-de-Haute-Provence, France), confirming the coexistence of tetraploid (28.2%) and octoploid cytotypes (71.2%), but also uncovering a small number of hexaploid individuals (0.6%). The analysis of repetitive elements from short-read genome-skimming data combined with nuclear (ITS) and whole plastid DNA sequences support an autopolyploid origin of the polyploid S. doronicum individuals and provide molecular evidence regarding the sole contribution of tetraploids in the formation of hexaploid individuals. The evolutionary impact and resilience of the new cytotype have yet to be determined, although the coexistence of different cytotypes may indicate nascent speciation. Full article

Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe. Full article