Using genomic repeats for phylogenomics: a case study in wild tomatoes (SolanumsectionLycopersicon: Solanaceae)

Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species

Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.

Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes

Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn't detect differences between subspecies, although (GAA)₁₀ signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.

Evolution, systematics, and the unnatural history of mitochondrial DNA

The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.

Phylogeny and biogeography of Myrcia sect. Aguava (Myrtaceae, Myrteae) based on phylogenomic and Sanger data provide evidence for a Cerrado origin and geographically structured clades

Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.

Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification

Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.

High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures

The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins’ structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitative Trait Loci) associated with reproductive and yield-related traits. The candidate genes/QTLs regulating heat tolerance in the selected landrace E42 could be further investigated to better understand the genetic mechanisms controlling traits for high and stable yield trait under high temperatures.

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

INTRODUCTION

Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.

RESULTS

(i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures.

CONCLUSION

We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.

Signaling pathway played by salicylic acid, gentisic acid, nitric oxide, polyamines and non-enzymatic antioxidants in compatible and incompatible Solanum-tomato mottle mosaic virus interactions

Plants are exposed to a vast array of pathogens. The interaction between them may be classified in compatible and incompatible. Polyamines (PAs) are involved in defense responses, as well as salicylic acid (SA), gentisic acid (GA) and nitric oxide (NO), which can increase the content of reactive oxygen species (ROS), creating a harsh environment to the pathogen. ROS can also damage the host cell and they can be controlled by ascorbate and glutathione. Among phytopathogens, one of the major threats to tomato crops is tomato mottle mosaic virus (ToMMV). Resistance against this virus probably involves the Tm-2² gene. This work aimed to analyze signaling and antioxidant molecules in the defense response against ToMMV in Solanum pimpinellifolium and in S. lycopersicum 'VFNT'. In S. pimpinellifolium plants inoculated with ToMMV, an increase in NO, SA, GA, ascorbate and oxidized glutathione and a decrease in the content of PAs were observed. Characteristic symptoms of diseased plants and high absorbance values in PTA-ELISA indicated a compatible interaction. In VFNT-inoculated plants, less significant differences were noticed. Symptoms and viral concentration were not detected, indicating an incompatible interaction, possibly associated with the effector-triggered immunity (ETI) response.

Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features

PREMISE

The origin of allopolyploids is believed to shape their evolutionary potential, ecology, and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides).

METHODS

We used a suite of approaches ranging from morphological, phylogenetic (three unlinked molecular markers), and cytogenetic analyses (in situ hybridization) to genome size screening and genome skimming.

RESULTS

Genotyping proved the expected parentage of all analyzed accessions of H. pallidiflorum and H. picroides and revealed that nearly all of them originated independently. Genome sizes and genome dosage largely corresponded to morphology, whereas the maternal origin of the allopolyploids had no discernable effect. Polyploid accessions of both parental species usually contained genetic material from other species. Given the phylogenetic distance of the parents, their chromosomes appeared only weakly differentiated in genomic in situ hybridization (GISH), as well as in overall comparisons of the repetitive fraction of their genomes. Furthermore, the repeatome of a phylogenetically more closely related species (H. umbellatum) differed significantly more.

CONCLUSIONS

We proved (1) multiple origins of hybridogeneous apomicts from the same diploid parental taxa, and (2) allopolyploid origins of polyploid accessions of the parental species. We also showed that the evolutionary dynamics of very fast evolving markers such as satellite DNA or transposable elements does not necessarily follow patterns of speciation.

Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae)

The unigeneric tribe Heliophileae encompassing more than 100 Heliophila species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity hotspots (Cape Floristic Region and Succulent Karoo). The monospecific Chamira (C. circaeoides), the only crucifer species with persistent cotyledons, is traditionally retrieved as the closest relative of Heliophileae. Our transcriptome analysis revealed a whole-genome duplication (WGD) ∼26.15-29.20 million years ago, presumably preceding the Chamira/Heliophila split. The WGD was then followed by genome-wide diploidization, species radiations, and cladogenesis in Heliophila. The expanded phylogeny based on nuclear ribosomal DNA internal transcribed spacer (ITS) uncovered four major infrageneric clades (A-D) in Heliophila and corroborated the sister relationship between Chamira and Heliophila. Herein, we analyzed how the diploidization process impacted the evolution of repetitive sequences through low-coverage whole-genome sequencing of 15 Heliophila species, representing the four clades, and Chamira. Despite the firmly established infrageneric cladogenesis and different ecological life histories (four perennials vs. 11 annual species), repeatome analysis showed overall comparable evolution of genome sizes (288-484 Mb) and repeat content (25.04-38.90%) across Heliophila species and clades. Among Heliophila species, long terminal repeat (LTR) retrotransposons were the predominant components of the analyzed genomes (11.51-22.42%), whereas tandem repeats had lower abundances (1.03-12.10%). In Chamira, the tandem repeat content (17.92%, 16 diverse tandem repeats) equals the abundance of LTR retrotransposons (16.69%). Among the 108 tandem repeats identified in Heliophila, only 16 repeats were found to be shared among two or more species; no tandem repeats were shared by Chamira and Heliophila genomes. Six "relic" tandem repeats were shared between any two different Heliophila clades by a common descent. Four and six clade-specific repeats shared among clade A and C species, respectively, support the monophyly of these two clades. Three repeats shared by all clade A species corroborate the recent diversification of this clade revealed by plastome-based molecular dating. Phylogenetic analysis based on repeat sequence similarities separated the Heliophila species to three clades [A, C, and (B+D)], mirroring the post-polyploid cladogenesis in Heliophila inferred from rDNA ITS and plastome sequences.

Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis

Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.

Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.

Comparative analysis of repetitive sequences among species from the potato and the tomato clades

BACKGROUND AND AIMS

The genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study we compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context.

METHODS

Genome skimming followed by a clustering approach was used as implemented in the RepeatExplorer pipeline. Repeat classes were annotated and the sequences of their main domains were compared.

KEY RESULTS

Repeat abundance and genome size were correlated and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements. Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements. Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile. There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species. Interspersed repeat profiles were very similar among potatoes. The repeat profile of Solanum etuberosum was more similar to that of the potato clade.

CONCLUSIONS

The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridization techniques.

Plant phylogenomics based on genome-partitioning strategies: Progress and prospects

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

Genome Size Diversity and Its Impact on the Evolution of Land Plants

Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps.

Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes

DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.

Phylogenomics of tomato chloroplasts using assembly and alignment-free method

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes

PREMISE OF THE STUDY

The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.

METHODS

Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes.

RESULTS

Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions.

DISCUSSION

Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)

Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila + N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.

Cuticular hydrocarbons and sucrose esters as chemotaxonomic markers of wild and cultivated tomato species (Solanum section Lycopersicon)

The tomato (Solanum lycopersicum L.) is one of the most important vegetables worldwide. Due to the limited genetic variability, wild related species are considered as potential gene pool for breeding cultivated plants with enriched genetic basis. Taxonomic relations between tomato species at the level of single groups and taxa still remain, however, not fully resolved. Hence, in addition to already reported classification based on the morphology of the plants and molecular markers, we proposed chemotaxonomic approach to unveil some aspects of tomato taxonomy. Cuticular hydrocarbons and surface sucrose esters (SEs) were used as chemotaxonomic markers. Classification based on the cuticular hydrocarbon profile was in good agreement with other taxonomic studies as long as between-species differences were taken into account. Clear separation of the common tomato and closely related species from the majority of S. pennellii accessions was obtained. In the same time, however, S. pennellii revealed broad variation: based on the results, three highly distinct types of these plants were proposed, among them one type was very similar to cultivated tomato and its relatives. Addition of SEs profiles to the dataset did not impair the classification, but clarified the position of S. pennellii. The results suggest possible hybrid origin of some of S. pennellii and wild S. lycopersicum accessions, and the approach proposed has a potential to identify such hybrid plant lines.