Genome Size Variation Research Articles

Insights into the Genomic Background of Nine Common Chinese Medicinal Plants by Flow Cytometry and Genome Survey

Medicinal plants have long played a crucial role in healthcare systems, but limited genomic information on these species has impeded the integration of modern biological technologies into medicinal plant research. In this study, we selected nine common medicinal plants, each belonging to a different plant family, including Sarcandra glabra (Chloranthaceae), Nekemias grossedentata (Vitaceae), Uraria crinita (Fabaceae), Gynostemma pentaphyllum (Cucurbitaceae), Reynoutria japonica (Polygonaceae), Pseudostellaria heterophylla (Caryophyllaceae), Morinda officinalis (Rubiaceae), Vitex rotundifolia (Lamiaceae), and Gynura formosana (Asteraceae), to estimate their genome sizes and conduct preliminary genomic surveys. The estimated genome sizes by flow cytometry were 3.66 Gb, 0.65 Gb, 0.58 Gb, 1.02 Gb, 3.96 Gb, 2.99 Gb, 0.43 Gb, 0.78 Gb, and 7.27 Gb, respectively. The genome sizes of M. officinalis, R. japonica, and G. pentaphyllum have been previously reported. Comparative analyses suggest that variations in genome size may arise due to differences in measurement methods and sample sources. Therefore, employing multiple approaches to assess genome size is necessary to provide more reliable information for further genomic research. Based on the genome survey, species with considerable genome size variation or polyploidy, such as G. pentaphyllum, should undergo a ploidy analysis in conjunction with population genomics studies to elucidate the development of the diversified genome size. Additionally, a genome survey of U. crinita, a medicinal plant with a relatively small genome size (509.08 Mb) and of considerable interest in southern China, revealed a low heterozygosity rate (0.382%) and moderate repeat content (51.24%). Given the limited research costs, this species represents a suitable candidate for further genomic studies on Leguminous medicinal plants characteristic of southern China. This foundational genomic information will serve as a critical reference for the sustainable development and utilization of these medicinal plants.

Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry

Aralia elata is closely related to Panax ginseng and contains high levels of saponins and other medicinal compounds. Successful A. elata micropropagation is commercially significant; however, the genomic stability of tissue culture-derived regenerants is unclear. In this study, callus-derived regenerated A. elata plants were obtained, and their cytogenomic constitutions were assessed. Using RepeatExplorer, pre-labeled oligonucleotide probes (PLOPs) were developed with newly mined tandem repeats from < 1× NGS whole-genome short reads, fluorescence in situ hybridization (FISH) was performed using six repeat probes, including three universal PLOPs, and genomic DNA content was estimated using flow cytometry. Regenerated A. elata plants (50) exhibited consistent ploidy, repeat distribution, and genome sizes compared with those exhibited by the mother plant. Six repeat probes were detected using FISH. Tandem repeat AeTR49 was identified as an excellent cytogenetic marker for homologous chromosomes, and AeTR161 and AeTR178 were localized in the centromeric and telomeric sections, respectively. Genomic DNA content (2C) was estimated at 2.46 ± 0.04 pg in the mother plant and 2.41 ± 0.05 pg in regenerated plants, with no significant variations in genome size or chromosome length. These results demonstrate that cytogenomics can be used to effectively evaluate chromosome-level genomic stability in regenerated A. elata plants.

Physiological and Molecular Mechanisms of Lepidopteran Insects: Genomic Insights and Applications of Genome Editing for Future Research.

Lepidopteran insects are a major threat to global agriculture, causing significant crop losses and economic damage. Traditional pest control methods are becoming less effective due to the rapid evolution of insecticide resistance. This study explores the current status and genomic characteristics of 1315 Lepidopteran records, alongside an overview of relevant research, utilizing advanced functional genomics techniques, including RNA-seq and CRISPR/Cas9 gene-editing technologies to uncover the molecular mechanisms underlying insecticide resistance. Our genomic analysis revealed significant variability in genome size, assembly quality, and chromosome number, which may influence species' biology and resistance mechanisms. We identified key resistance-associated genes and pathways, including detoxification and metabolic pathways, which help these insects evade chemical control. By employing CRISPR/Cas9 gene-editing techniques, we directly manipulated resistance-associated genes to confirm their roles in resistance, demonstrating their potential for targeted interventions in pest management. These findings emphasize the value of integrating genomic data into the development of effective and sustainable pest control strategies, reducing reliance on chemical insecticides and promoting environmentally friendly integrated pest management (IPM) approaches. Our study highlights the critical role of functional genomics in IPM and its potential to provide long-term solutions to the growing challenge of Lepidopteran resistance.

Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma.

Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.

Evolutionary history written in tandem arrays – satellite repeats in the Lagoseris lineage of Crepis sensu lato (Asteraceae)

Abstract Satellite DNA families are excellent markers in evolutionary studies of plant karyotypes. Together with phylogenetic background, they can provide additonal information on different scenarios accompanying the speciation and diversification of related species. The Lagoseris lineage of Crepis sensu lato constitutes an interesting model in such studies, mainly due to: (i) the presence of large chromosomes; (ii) several base chromosome numbers; and (iii) variation in genome sizes. We aimed to characterize the satellite families and compare their genomic and chromosomal organization to better understand the evolutionary pathways that shaped the genomes of the Lagoseris lineage. Eight different families of satellite repeats were identified in Crepis palaestina based on RepeatExplorer raw Illumina read analyses. Most of these satellites were present in five species studied from the Lagoseris lineage and organized in tandem arrays. If the particular repeat was present in the genome of the related species, its genomic organization showed similarity to the one observed in C. palaestina. This similar genomic organization was not often reflected at the chromosomal level, where many distinct distribution patterns were shown, from several major loci to numerous minor ones spread throughout the chromosomal arms. The evolution of satellite repeats is discussed in phylogenetic context.

Spatial and Temporal Variation of Precipitation Drives the Genome Size Variation in Scolopendra in Chinese Mainland.

Genome size is an adaptive trait, and its variations influence the organismal phenotype and fitness. In this study, we propose a hypothesis linking variations in genome size within Scolopendra to ecological factors. To test this hypothesis, we employed flow cytometry to estimate genome size in seven Scolopendra species from Chinese mainland. Subsequently, we reconstructed the phylogenetic relationship of these species using the cytochrome c oxidase subunit 1 gene and conducted phylogenetic comparative analysis to assess the relationships between genome size and niche breadth or 19 bioclimatic variables. Our findings indicate the following: (1) genome size in Scolopendra can be categorized into three groups, similar to the phylogenetic clades; (2) there is a negative correlation between genome size in Scolopendra species and the precipitation niche breadth of species; (3) the estimated divergence time of Scolopendra dates back 153 Mya, during the Jurassic period. We assume that consistent aridity geological periods may promote the evolution of Scolopendra species with a large genome size, whereas rapidly fluctuating humidity geological periods may have the opposite effect.

Biotic and abiotic factors associated with genome size evolution in oaks.

The evolutionary processes that underlie variation in plant genome size have been much debated. Abiotic factors are thought to have played an important role, with negative and positive correlations between genome size and seasonal or stressful climatic conditions being reported in several systems. In turn, variation in genome size may influence plant traits which affect interactions with other organisms, such as herbivores. The mechanisms underlying evolutionary linkages between plant genome size and biotic and abiotic factors nonetheless remain poorly understod. To address this gap, we conducted phylogenetically controlled analyses testing for associations between genome size, climatic variables, plant traits (defenses and nutrients), and herbivory across 29 oak (Quercus) species. Genome size is significantly associated with both temperature and precipitation seasonality, whereby oak species growing in climates with lower and less variable temperatures but more variable rainfall had larger genomes. In addition, we found a negative association between genome size and leaf nutrient concentration (found to be the main predictor of herbivory), which in turn led to an indirect effect on herbivory. A follow-up test suggested that the association between genome size and leaf nutrients influencing herbivory was mediated by variation in plant growth, whereby species with larger genomes have slower growth rates, which in turn are correlated with lower nutrients. Collectively, these findings reveal novel associations between plant genome size and biotic and abiotic factors that may influence life history evolution and ecological dynamics in this widespread tree genus.

Koliella bifissiva sp. nov (Chlorellaceae, Chlorophyta) and Analysis of Its Organelle Genomes.

Chlorellacean members are common in aquatic or subaerial habitats, and many of them have significant economic value. Taxonomic reports and organelle genome data for the Nannochloris clade, an important subgroup within this family, are limited, hindering the understanding and exploitation of this clade. In this study, a fusiform-celled strain, FACHB-3607, was isolated from a pond in China. Through examination of morphological characteristics and phylogenetic analyses of rbcL, 18S rDNA, and ITS, it was identified as a new species within the Nannochloris clade, named Koliella bifissiva sp. nov. In addition, this study provided a first insight into the organellar genomes of the genus Koliella. The K. bifissiva chloroplast had a 99.8 kb genome, and the mitochondrion had a 40.8 kb genome, which are moderate sizes within the Nannochloris clade. Phylogenomic analysis showed that K. bifissiva is most closely related to Nannochloris sp. "desiccata", followed by Marvania. In contrast, Picochlorum was the most distantly related species. The organelle genomes of the Nannochloris clade display dynamic evolution, reflected in variations in genome size, gene content and order, and selection pressure. This research enhances our knowledge of species diversity and evolutionary history in the Nannochloris clade.

Uncovering the genomic diversity of the wild forage crop Setaria sphacelata

AbstractGrasses are considered one of the most important angiosperm groups in economic terms. The Setaria sphacelata complex is an intriguing species with considerable variation in genome size (GS). It is currently being explored from a genomic perspective especially because of its great adaptability under winter periods. Repetitive DNA sequences are known to contribute significantly to GS diversity, which in turn can play a role in impacting the ecology and evolution of a species. This study is aimed to characterize the GS and repetitive elements of different germplasm accessions of S. sphacelata. We analyzed 540 plants from 70 accessions collected worldwide. Flow cytometry was used for GS estimation, together with chromosome counting, fluorescent in situ hybridization (FISH), and bioinformatic analysis. Most (i.e., 80%) accessions were tetraploids (2n = 4x = 36) with GS ranging from 3.0 to 3.7 pg/2C. Additionally, a low number of diploids (2n = 2x = 18; ∼1.6 to 2 pg/2C), pentaploids (2n = 5x = 45: ∼4 pg/2C), hexaploids (2n = 6x = 54; ∼4.4 pg/2C), and octoploids (2n = 8x = 72; ∼6 pg/2C,) were detected. The greatest variation was found in accessions from South Africa. RepeatExplorer2 showed that 39% and 43% of the genomes of two diploid accessions comprised repetitive sequences, with Ty3/gypsy retrotransposons being the most abundant repeats. However, variation in the percentage of two Ty3/gypsy sublineages, Athila and Ogre, suggests different process of amplification and deletion of repeats during the evolution of the species complex. In contrast, FISH revealed some satellite repeats with a conserved localized distribution in pericentromeric regions between accessions. Although differences in the distribution of the FISH signals over the chromosomes were observed between the different ploidy levels, the data suggest that increases in the ploidy level were associated with the occurrence of hybridization and DNA loss.

Genetic diversification of allohexaploid Brassica hybrids (AABBCC) using a fertile octoploid with excessive C genome set (AABBCCCC).

Using octoploid somatic hybrids with excessive C genome sets, AABBCCCC, a diverse allohexaploid, AABBCC, was produced by C genome reduction through subsequent crossing with various AABB cultivars. Even when somatic hybrids are produced, the plants that are produced are rarely in themselves an innovative crop. In this study, we used somatic hybrids of Brassica juncea (AABB) and B. oleracea (CC) as model cases for the genetic diversification of the somatic hybrids. One cell of 'Akaoba Takana' (B. juncea) and two cells of 'Snow Crown' (B. oleracea) were fused to create several somatic hybrids with excessive C genomes, AABBCCCC. Using AABBCCCC somatic hybrids as mother plants and crossing with 'Akaoba Takana', the AABBCC progenies were generated. When these AABBCC plants were self-fertilized, and flow cytometric (FCM) analysis was performed on the next generations, differences in the relative amount of genome size variation were observed, depending on the different AABBCCCC parents used for AABBCC creation. Further self-progeny was obtained for AABBCC plants with a theoretical allohexaploid DNA index by FCM. However, as the DNA indices of the progeny populations varied between plants used and aneuploid individuals still occurred in the progeny populations, it was difficult to say that the allohexaploid genome was fully stabilized. Next, to obtain genetic diversification of the allohexaploid, different cultivars of B. juncea were crossed with AABBCCCC, resulting in diverse AABBCC plants. Genetic diversity can be further expanded by crossbreeding plants with different AABBCC genome sets. Although genetic stability is necessary to ensure in the later generations, the results obtained in this study show that the use of somatic hybrids with excess genomes is an effective strategy for creating innovative crops.

Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses.

Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the "polyploid genome shock hypothesis" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.

Deciphering Pteronia's evolution in the Cape Floristic Region: A comprehensive study disputes polyploid deficiency and affirms diploid radiation.

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS-based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low-copy nuclear genes confirm Pteronia as a well-supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C-value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.

Comparative Analysis of Chloroplast Genomes in Cephaleuros and Its Related Genus (Trentepohlia): Insights into Adaptive Evolution.

Cephaleuros species are well-known as plant pathogens that cause red rust or algae spot diseases in many economically cultivated plants that grow in shady and humid environments. Despite their prevalence, the adaptive evolution of these pathogens remains poorly understood. We sequenced and characterized three Cephaleuros (Cephaleuros lagerheimii, Cephaleuros diffusus, and Cephaleuros virescens) chloroplast genomes, and compared them with seven previously reported chloroplast genomes. The chloroplast sequences of C. lagerheimii, C. diffusus, and C. virescens were 480,613 bp, 383,846 bp, and 472,444 bp in length, respectively. These chloroplast genomes encoded 94 genes, including 27 tRNA genes, 3 rRNA genes, and 64 protein-coding genes. Comparative analysis uncovered that the variation in genome size was principally due to the length of intergenic spacer sequences, followed by introns. Furthermore, several highly variable regions (trnY-GTA, trnL-TAG, petA, psbT, trnD-GTC, trnL-TAA, ccsA, petG, psaA, psaB, rps11, rps2, and rps14) were identified. Codon bias analysis revealed that the codon usage pattern of Cephaleuros is predominantly shaped by natural selection. Additionally, six chloroplast protein-coding genes (atpF, chlN, psaA, psaB, psbA, and rbcL) were determined to be under positive selection, suggesting they may play a vital roles in the adaptation of Cephaleuros to low-light intensity habitats.

Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.

Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers.

Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known. A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models. The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution. Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.

Retraction Note: Genetic basis of genome size variation of wheat.

Retraction Note: Genetic basis of genome size variation of wheat.

Genome Size Variation in Sesamum indicum L. Germplasm from Niger.

Sesamum indicum L. (Pedaliaceae) is one of the most economically important oil crops in the world, thanks to the high oil content of its seeds and its nutritional value. It is cultivated all over the world, mainly in Asia and Africa. Well adapted to arid environments, sesame offers a good opportunity as an alternative subsistence crop for farmers in Africa, particularly Niger, to cope with climate change. For the first time, the variation in genome size among 75 accessions of the Nigerien germplasm was studied. The sample was collected throughout Niger, revealing various morphological, biochemical and phenological traits. For comparison, an additional accession from Thailand was evaluated as an available Asian representative. In the Niger sample, the 2C DNA value ranged from 0.77 to 1 pg (753 to 978 Mbp), with an average of 0.85 ± 0.037 pg (831 Mbp). Statistical analysis showed a significant difference in 2C DNA values among 58 pairs of Niger accessions (p-value < 0.05). This significant variation indicates the likely genetic diversity of sesame germplasm, offering valuable insights into its possible potential for climate-resilient agriculture. Our results therefore raise a fundamental question: is intraspecific variability in the genome size of Nigerien sesame correlated with specific morphological and physiological traits?

Diversity and evolution of transposable elements in the plant-parasitic nematodes

BackgroundTransposable elements (TEs) are mobile DNA sequences that propagate within genomes, occupying a significant portion of eukaryotic genomes and serving as a source of genetic variation and innovation. TEs can impact genome dynamics through their repetitive nature and mobility. Nematodes are incredibly versatile organisms, capable of thriving in a wide range of environments. The plant-parasitic nematodes are able to infect nearly all vascular plants, leading to significant crop losses and management expenses worldwide. It is worth noting that plant parasitism has evolved independently at least three times within this nematode group. Furthermore, the genome size of plant-parasitic nematodes can vary substantially, spanning from 41.5 Mbp to 235 Mbp. To investigate genome size variation and evolution in plant-parasitic nematodes, TE composition, diversity, and evolution were analysed in 26 plant-parasitic nematodes from 9 distinct genera in Clade IV.ResultsInterestingly, despite certain species lacking specific types of DNA transposons or retrotransposon superfamilies, they still exhibit a diverse range of TE content. Identification of species-specific TE repertoire in nematode genomes provides a deeper understanding of genome evolution in plant-parasitic nematodes. An intriguing observation is that plant-parasitic nematodes possess extensive DNA transposons and retrotransposon insertions, including recent sightings of LTR/Gypsy and LTR/Pao superfamilies. Among them, the Gypsy superfamilies were found to encode Aspartic proteases in the plant-parasitic nematodes.ConclusionsThe study of the transposable element (TE) composition in plant-parasitic nematodes has yielded insightful discoveries. The findings revealed that certain species exhibit lineage-specific variations in their TE makeup. Discovering the species-specific TE repertoire in nematode genomes is a crucial element in understanding the evolution of genomes in plant-parasitic nematodes. It allows us to gain a deeper insight into the intricate workings of these organisms and their genetic makeup. With this knowledge, we are gaining a fundamental piece in the puzzle of understanding the evolution of these parasites. Moreover, recent transpositions have led to the acquisition of new TE superfamilies, especially Gypsy and Pao retrotransposons, further expanding the diversity of TEs in these nematodes. Significantly, the widely distributed Gypsy superfamily possesses proteases that are exclusively associated with parasitism during nematode-host interactions.These discoveries provide a deeper understanding of the TE landscape within plant-parasitic nematodes.

Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution.

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.

Genome size variation in Cape schoenoid sedges (Schoeneae) and its ecophysiological consequences.

Increases in genome size in plants-often associated with larger, low-density stomata and greater water-use efficiency (WUE)-could affect plant ecophysiological and hydraulic function. Variation in plant genome size is often due to polyploidy, having occurred repeatedly in the austral sedge genus Schoenus in the Cape Floristic Region (CFR), while species in the other major schoenoid genus in the region, Tetraria, have smaller genomes. Comparing these genera is useful as they co-occur at the landscape level, under broadly similar bioclimatic conditions. We hypothesized that CFR Schoenus have greater WUE, with lower maximum stomatal conductance (gwmax) imposed by larger, less-dense stomata. We investigated relationships between genome size and stomatal parameters in a phylogenetic context, reconstructing a phylogeny of CFR-occurring Schoeneae (Cyperaceae). Species' stomatal and functional traits were measured from field-collected and herbarium specimens. Carbon stable isotopes were used as an index of WUE. Genome size was derived from flow-cytometric measurements of leafy shoots. Evolutionary regressions demonstrated that stomatal size and density covary with genome size, positively and negatively, respectively, with genome size explaining 72-75% of the variation in stomatal size. Larger-genomed species had lower gwmax and C:N ratios, particularly in culms. We interpret differences in vegetative physiology between the genera as evidence of more-conservative strategies in CFR Schoenus compared to the more-acquisitive Tetraria. Because Schoenus have smaller, reduced leaves, they likely rely more on culm photosynthesis than Tetraria. Across the CFR Schoeneae, ecophysiology correlates with genome size, but confounding sources of trait variation limit inferences about causal relationships between traits.