Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

A multidisciplinary and integrative review of the structural genome and epigenome of Capsicum L. species

MAIN CONCLUSION

We revised and integrated the genomic and epigenomic data into a comparative Capsicum ideogram, evidencing the advances and future perspectives. Capsicum L. (Solanaceae) genome has been characterized concerning karyotype, nuclear and chromosomal genome size, genome sequencing and physical mapping. In addition, the epigenome has been investigated, showing chromosomal distribution of epimarks in histone amino acids. Genetic and epigenetic discoveries have given light to understanding the structure and organization of the Capsicum "omics". In addition, interspecific and intraspecific similarities and diversities have been identified, characterized and compared in taxonomic and evolutive scenarios. The journey through Capsicum studies allows us to know the 2n = 2x = 24 and 2n = 2x = 26 chromosome numbers, as well as the relatively homomorphic karyotype, and the 1C chromosomal DNA content. In addition, Capsicum "omics" diversity has mainly been evidenced from the nuclear 1C value, as well as from repeatome composition and mapping. Like this, Capsicum provides several opportunities for "omics", ecological, agronomic and conservation approaches, as well as subjects that can be used at different levels of education. In this context, we revisit and integrate Capsicum data about the genome size, karyotype, sequencing and cytogenomics, pointing out the progress and impact of this knowledge in taxonomic, evolutive and agronomic contexts. We also noticed gaps, which can be a focus of further studies. From this multidisciplinary and integrative review, we intend to show the beauty and intrigue of the Capsicum genome and epigenome, as well as the outcomes of these similarities and differences.

Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication

BACKGROUND AND AIMS

Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analysed six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias' evolutionary paths and can guide breeding initiatives.

METHODS

We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as the evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole-genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multicolour FISH.

KEY RESULTS

The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes.

CONCLUSIONS

Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and guiding future hortensia breeding.

BeetRepeats: reference sequences for genome and polymorphism annotation in sugar beet and wild relatives

OBJECTIVES

Despite the advances in genomics, repetitive DNAs (repeats) are still difficult to sequence, assemble, and identify. This is due to their high abundance and diversity, with many repeat families being unique to the organisms in which they were described. In sugar beet, repeats make up a significant portion of the genome (at least 53%), with many repeats being restricted to the beet genera, Beta and Patellifolia. Over the course of over 30 years and many repeat-based studies, over a thousand reference repeat sequences for beet genomes have been identified and many experimentally characterized (e.g. physically located on the chromosomes). Here, we present the collection of these reference repeat sequences for beets.

DATA DESCRIPTION

The BeetRepeats_v1.0 resource is a comprehensive compilation of all characterized repeat families, including satellite DNAs, ribosomal DNAs, transposable elements and endogenous viruses. The genomes covered are those of sugar beet and closely related wild beets (genera Beta and Patellifolia) as well as Chenopodium quinoa and Spinacia oleracea (all belonging to the Amaranthaceae). The reference sequences are in fasta format and comprise well-characterized repeats from both repeat categories (dispersed/mobile as well as tandemly arranged). The database is suitable for the RepeatMasker and RepeatExplorer2 pipelines and can be used directly for any repeat annotation and repeat polymorphism detection purposes.

Satellite DNAs and the evolution of the multiple X1X2Y sex chromosomes in the wolf fish Hoplias malabaricus (Teleostei; Characiformes)

Multiple sex chromosomes usually arise from chromosomal rearrangements which involve ancestral sex chromosomes. There is a fundamental condition to be met for their long-term fixation: the meiosis must function, leading to the stability of the emerged system, mainly concerning the segregation of the sex multivalent. Here, we sought to analyze the degree of differentiation and meiotic pairing properties in the selected fish multiple sex chromosome system present in the wolf-fish Hoplias malabaricus (HMA). This species complex encompasses seven known karyotype forms (karyomorphs) where the karyomorph C (HMA-C) exhibits a nascent XY sex chromosomes from which the multiple X1X2Y system evolved in karyomorph HMA-D via a Y-autosome fusion. We combined genomic and cytogenetic approaches to analyze the satellite DNA (satDNA) content in the genome of HMA-D karyomorph and to investigate its potential contribution to X1X2Y sex chromosome differentiation. We revealed 56 satDNA monomers of which the majority was AT-rich and with repeat units longer than 100 bp. Seven out of 18 satDNA families chosen for chromosomal mapping by fluorescence in situ hybridization (FISH) formed detectable accumulation in at least one of the three sex chromosomes (X1, X2 and neo-Y). Nine satDNA monomers showed only two hybridization signals limited to HMA-D autosomes, and the two remaining ones provided no visible FISH signals. Out of seven satDNAs located on the HMA-D sex chromosomes, five mapped also to XY chromosomes of HMA-C. We showed that after the autosome-Y fusion event, the neo-Y chromosome has not substantially accumulated or eliminated satDNA sequences except for minor changes in the centromere-proximal region. Finally, based on the obtained FISHpatterns, we speculate on the possible contribution of satDNA to sex trivalent pairing and segregation.

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.

Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution

Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus)

BACKGROUND

Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes.

RESULTS

In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA.

CONCLUSIONS

Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Mitigating Salinity Stress in Quinoa (Chenopodium quinoa Willd.) with Biochar and Superabsorber Polymer Amendments

In agriculture, soil amendments are applied to improve soil quality by increasing the water retention capacity and regulating the pH and ion exchange. Our study was carried out to investigate the impact of a commercial biochar (Bc) and a superabsorbent polymer (SAP) on the physiological and biochemical processes and the growth performance of Chenopodium quinoa (variety ICBA-5) when exposed to high salinity. Plants were grown for 25 days under controlled greenhouse conditions in pots filled with a soil mixture with or without 3% Bc or 0.2% SAP by volume before the initiation of 27 days of growth in hypersaline conditions, following the addition of 300 mM NaCl. Without the Bc or soil amendments, multiple negative effects of hypersalinity were detected on photosynthetic CO2 assimilation (Anet minus 70%) and on the production of fresh matter from the whole plant, leaves, stems and roots (respectively, 55, 46, 64 and 66%). Moreover, increased generation of reactive oxygen species (ROS) was indicated by higher levels of MDA (plus 142%), antioxidant activities and high proline levels (plus 311%). In the pots treated with 300 mM NaCl, the amendments Bc or SAP improved the plant growth parameters, including fresh matter production (by 10 and 17%), an increased chlorophyll content by 9 and 13% and Anet in plants (by 98 and 115%). Both amendments (Bc and SAP) resulted in significant salinity mitigation effects, decreasing proline and malondialdehyde (MDA) levels whilst increasing both the activity of enzymatic antioxidants and non-enzymatic antioxidants that reduce the levels of ROS. This study confirms how soil amendments can help to improve plant performance and expand the productive range into saline areas.

Preparation of Mitotic Chromosomes with the Dropping Technique

The quality of chromosome preparation influences all downstream analyses and is therefore crucial. Hence, numerous protocols exist to produce microscopic slides with mitotic chromosomes. Nevertheless, due to the high content of fibers in and around a plant cell, preparation of plant chromosomes is still far from trivial and needs to be fine-tuned for each species and tissue type. Here, we outline the "dropping method," a straightforward and efficient protocol to prepare multiple slides with uniform quality from a single chromosome preparation. In this method, nuclei are extracted and cleaned to produce a nuclei suspension. In a drop-by-drop manner, this suspension is then applied from a certain height onto the slides, causing the nuclei to rupture and the chromosomes to spread. Due to the physical forces that accompany the dropping and spreading process, this method is best suited for species with small- to medium-sized chromosomes.

Measuring the Invisible: The Sequences Causal of Genome Size Differences in Eyebrights (Euphrasia) Revealed by k-mers

Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation is challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies by design miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole-genome sequencing data of diploid eyebrights (Euphrasia), a group of plants that have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further match high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find genome size differences of up to 230Mbp, equivalent to more than 20% genome size variation. The largest contributions to these differences come from rDNA sequences, a 145-nt genomic satellite and a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class (copy number ≤ 10×) of up to 27 Mbp, possibly indicating differences in gene space between our samples. We demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without the use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats if they aim to characterise the full range of genomic variants. To allow future work with other taxonomic groups, we share our k-mer analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.)

Quinoa is a pseudocereal originating from the Andean regions. Despite quinoa's long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize quantitative trait loci (QTL) contributing to the phenotypic variation of agronomically important traits. We crossed the Chilean accession PI-614889 and the Peruvian accession CHEN-109, which depicted significant differences in days to flowering, days to maturity, plant height, panicle length, and thousand kernel weight (TKW), saponin content, and mildew susceptibility. We observed sizeable phenotypic variation across F2 plants and F3 families grown in the greenhouse and the field, respectively. We used Skim-seq to genotype the F2 population and constructed a high-density genetic map with 133,923 single nucleotide polymorphism (SNPs). Fifteen QTL were found for ten traits. Two significant QTL, common in F2 and F3 generations, depicted pleiotropy for days to flowering, plant height, and TKW. The pleiotropic QTL harbored several putative candidate genes involved in photoperiod response and flowering time regulation. This study presents the first high-density genetic map of quinoa that incorporates QTL for several important agronomical traits. The pleiotropic loci can facilitate marker-assisted selection in quinoa breeding programs.

Early responses to salt stress in quinoa genotypes with opposite behavior

Soil salinity is among the major abiotic stresses that plants must cope with, mainly in arid and semiarid regions. The tolerance to high salinity is an important agronomic trait to sustain food production. Quinoa is a halophytic annual pseudo-cereal species with high nutritional value that can secrete salt out of young leaves in external non-glandular cells called epidermal bladder cells (EBC). Previous work showed high salt tolerance, but low EBC density was associated with an improved response in the early phases of salinity stress, mediated by tissue-tolerance traits mainly in roots. We compared the transcript profiling of two quinoa genotypes with contrasting salt tolerance patterning to identify the candidate genes involved in the differentially early response among genotypes. The transcriptome profiling, supported by in vitro physiological analyses, provided insights into the early-stage molecular mechanisms, both at the shoot and root level, based on the sensitive/tolerance traits. Results showed the presence of numerous differentially expressed genes among genotypes, tissues, and treatments, with genes involved in hormonal and stress response upregulated mainly in the sensitive genotype, suggesting that tolerance may be correlated to restricted changes in gene expression, at least after a short salt stress. These data, showing constitutive differences between the two genotypes, represent a solid basis for further studies to characterize the salt tolerance traits. Additionally, new information provided by this work might be useful for the development of plant breeding or genome engineering programs in quinoa.

Quinoa genome assembly employing genomic variation for guided scaffolding

We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.

Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa)

BACKGROUND

Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional balance. It is an allotetraploid species (AABB, 2n = 4x = 36) formed by the hybridization between AA and BB genome diploid (2n = 2x = 18) species. This study reports genetic studies in Chenopodium ficifolium as a potential B genome diploid model system to simplify the genetic studies of quinoa including gene identification and marker-assisted breeding.

RESULTS

Portsmouth, New Hampshire and Quebec City, Quebec accessions of C. ficifolium were used to develop an F2 population segregating for agronomically relevant traits including flowering time, plant height, the number of branches, branch angle, and internode length. Marker-trait associations were identified for the FLOWERING LOCUS T-LIKE 1 (FTL1) marker gene, where the alternate alleles (A1/A2) were segregating among the F2 generation plants in association with flowering time, plant height, and the number of branches. There was a strong correlation of the flowering time trait with both plant height and the number of branches. Thus, a possible multifaceted functional role for FTL1 may be considered. The parental Portsmouth and Quebec City accessions were homozygous for the alternate FTL1 alleles, which were found to be substantially diverged. SNPs were identified in the FTL1 coding sequence that could have some functional significance in relation to the observed trait variation.

CONCLUSION

These results draw further attention to the possible functional roles of the FTL1 locus in Chenopodium and justify continued exploration of C. ficifolium as a potential diploid model system for the genetic study of quinoa. We expect our findings to aid in quinoa breeding as well as to any studies related to the Chenopodium genus.

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

BACKGROUND AND AIMS

Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species.

METHODS

We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples.

KEY RESULTS

We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small.

CONCLUSIONS

We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

Background

In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them.

Results

We determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them.

Conclusions

The presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07853-2.

The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits

Cultivation of quinoa (Chenopodium quinoa), an annual pseudocereal crop that originated in the Andes, is spreading globally. Because quinoa is highly nutritious and resistant to multiple abiotic stresses, it is emerging as a valuable crop to provide food and nutrition security worldwide. However, molecular analyses have been hindered by the genetic heterogeneity resulting from partial outcrossing. In this study, we generated 136 inbred quinoa lines as a basis for the molecular identification and characterization of gene functions in quinoa through genotyping and phenotyping. Following genotyping-by-sequencing analysis of the inbred lines, we selected 5,753 single-nucleotide polymorphisms (SNPs) in the quinoa genome. Based on these SNPs, we show that our quinoa inbred lines fall into three genetic sub-populations. Moreover, we measured phenotypes, such as salt tolerance and key growth traits in the inbred quinoa lines and generated a heatmap that provides a succinct overview of the genotype–phenotype relationship between inbred quinoa lines. We also demonstrate that, in contrast to northern highland lines, most lowland and southern highland lines can germinate even under high salinity conditions. These findings provide a basis for the molecular elucidation and genetic improvement of quinoa and improve our understanding of the evolutionary process underlying quinoa domestication.

Subgenome evolution in allotetraploid plants

Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.

A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed

Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.

Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity

For a long time, the Cyperid clade (Thurniceae-Juncaceae-Cyperaceae) was considered a group of species possessing holocentromeres exclusively. The basal phylogenetic position of Prionium serratum (Thunb.) Drège (Thurniceae) within Cyperids makes this species an important specimen to understand the centromere evolution within this clade. In contrast to the expectation, the chromosomal distribution of the centromere-specific histone H3 (CENH3), alpha-tubulin and different centromere-associated post-translational histone modifications (H3S10ph, H3S28ph and H2AT120ph) demonstrate a monocentromeric organisation of P. serratum chromosomes. Analysis of the high-copy repeat composition resulted in the identification of two centromere-localised satellite repeats. Hence, monocentricity was the ancestral condition for the Juncaceae-Cyperaceae-Thurniaceae Cyperid clade, and holocentricity in this clade has independently arisen at least twice after differentiation of the three families, once in Juncaceae and the other one in Cyperaceae. In this context, methods suitable for the identification of holocentromeres are discussed.

The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the "library hypothesis"

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.

Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.

Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.