GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis

Prospective identification of extracellular triacylglycerol hydrolase with conserved amino acids in Amycolatopsis tolypomycina's high G+C genomic dataset

Extracellular triacylglycerol hydrolases (ETH) play a critical role for microorganisms, acting as essential tools for lipid breakdown and survival in challenging environments. The pursuit of more effective ETH genes and enzymes through evolution holds significant potential for enhancing living conditions. This study employs a proteogenomic approach to identify high G+C ETH in a notable Gram-positive bacterium, Amycolatopsis tolypomycina. Utilizing knowledge from genome and machine learning algorithms, prospective ETH genes/enzymes were identified. Notably, the ETH structural conserved accessibility to solvent clearly indicated the specific sixteen residues (GLY50, PRO93, GLY141, ASP148, GLY151, ASP172, ALA176, GLY195, TYR196, SER197, GLN198, GLY199, GLY200, GLY225, PRO327, ASP336) with no frequency. By pinpointing key residues and understanding their role, this study sets the stage for enhancing ETH performance through computational proteogenomic and contributes to the broader field of enzyme engineering, facilitating the development of more efficient and versatile ETH enzymes tailored to specific industrial or environmental contexts.

Evolution of Plant Genome Size and Composition

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.

Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes

During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5' to 3' untranslated regions, are enriched in hotspots, but this has been characterized in a handful of species only. We also lack a clear description of fine-scale variation in recombination rates within genic regions and little is known about hotspot position and intensity in plants. To address this question, we constructed fine-scale recombination maps from genetic polymorphism data and inferred recombination hotspots in 11 plant species. We detected gradients of recombination in genic regions in most species, yet gradients varied in intensity and shape depending on specific hotspot locations and gene structure. To further characterize recombination gradients, we decomposed them according to gene structure by rank and number of exons. We generalized the previously observed pattern that recombination hotspots are organized around the boundaries of coding sequences, especially 5' promoters. However, our results also provided new insight into the relative importance of the 3' end of genes in some species and the possible location of hotspots away from genic regions in some species. Variation among species seemed driven more by hotspot location among and within genes than by differences in size or intensity among species. Our results shed light on the variation in recombination rates at a very fine scale, revealing the diversity and complexity of genic recombination gradients emerging from the interaction between hotspot location and gene structure.

Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus

Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.

Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

Genome composition and GC content influence loci distribution in reduced representation genomic studies

BACKGROUND

Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored.

RESULTS

Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected.

CONCLUSIONS

Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

Compositional shifts associated with major evolutionary transitions in plants

Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both nucleotide and amino acids across a recent large-scale transcriptomic dataset for plants. We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes.

An alternative angiosperm DGAT1 topology and potential motifs in the N-terminus

The highly variable cytoplasmic N-terminus of the plant diacylglycerol acyltransferase 1 (DGAT1) has been shown to have roles in oligomerization as well as allostery; however, the biological significance of the variation within this region is not understood. Comparing the coding sequences over the variable N-termini revealed the Poaceae DGAT1s contain relatively high GC compositional gradients as well as numerous direct and inverted repeats in this region. Using a variety of reciprocal chimeric DGAT1s from angiosperms we show that related N-termini had similar effects (positive or negative) on the accumulation of the recombinant protein in Saccharomyces cerevisiae. When expressed in Camelina sativa seeds the recombinant proteins of specific chimeras elevated total lipid content of the seeds as well as increased seed size. In addition, we combine N- and C-terminal as well as internal tags with high pH membrane reformation, protease protection and differential permeabilization. This led us to conclude the C-terminus is in the ER lumen; this contradicts earlier reports of the cytoplasmic location of plant DGAT1 C-termini.

Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum), and Its Comparison with Other Solanaceae Species

Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources.

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.

GC content of plant genes is linked to past gene duplications

The frequency of G and C nucleotides in genomes varies from species to species, and sometimes even between different genes in the same genome. The monocot grasses have a bimodal distribution of genic GC content absent in dicots. We categorized plant genes from 5 dicots and 4 monocot grasses by synteny to related species and determined that syntenic genes have significantly higher GC content than non-syntenic genes at their 5`-end in the third position within codons for all 9 species. Lower GC content is correlated with gene duplication, as lack of synteny to distantly related genomes is associated with past interspersed gene duplications. Two mutation types can account for biased GC content, mutation of methylated C to T and gene conversion from A to G. Gene conversion involves non-reciprocal exchanges between homologous alleles and is not detectable when the alleles are identical or heterozygous for presence-absence variation, both likely situations for genes duplicated to new loci. Gene duplication can cause production of siRNA which can induce targeted methylation, elevating mC→T mutations. Recently duplicated plant genes are more frequently methylated and less likely to undergo gene conversion, each of these factors synergistically creating a mutational environment favoring AT nucleotides. The syntenic genes with high GC content in the grasses compose a subset that have undergone few duplications, or for which duplicate copies were purged by selection. We propose a “biased gene duplication / biased mutation” (BDBM) model that may explain the origin and trajectory of the observed link between duplication and genic GC bias. The BDBM model is supported by empirical data based on joint analyses of 9 angiosperm species with their genes categorized by duplication status, GC content, methylation levels and functional classes.

A positive correlation between GC content and growth temperature in prokaryotes

BACKGROUND

GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate.

RESULTS

With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation.

CONCLUSIONS

This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

Coding regions have complex interactions among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes, but the decrease only starts from the ∼ 25th codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating a universal selection for energy efficiency toward the N-termini of encoded proteins. Within a genome, the decreasing GC gradient is intensified from lowly to highly expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradients at four-fold and two-fold synonymous sites vary across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences, especially efficient energy usage.

Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis

Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.

Population Genomics on the Fly: Recent Advances in Drosophila

Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes

Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genomes. We explored the mechanisms maintaining the GC content in angiosperm plastomes, with a particular focus on the hypothesis of phylogenetic dependence and the correlation with deletion mutations. We measured three genetic traits, namely, GC content, A/T tracts, and G/C tracts, in the coding region of plastid genomes for 1382 angiosperm species representing 350 families and 64 orders, and tested the phylogenetic signal. Then, we performed correlation analyses and revealed the variation in evolutionary rate of selected traits using RRphylo. The plastid GC content in the coding region varied from 28.10% to 43.20% across angiosperms, with a few non-photosynthetic species showing highly reduced values, highlighting the significance of functional constraints. We found strong phylogenetic signal in A/T tracts, but weak ones in GC content and G/C tracts, indicating adaptive potential. GC content was positively and negatively correlated with G/C and A/T tracts, respectively, suggesting a trade-off between these two deletion events. GC content evolved at various rates across the phylogeny, with significant increases in monocots and Lamiids, and a decrease in Fabids, implying the effects of some other factors. We hypothesize that variation in plastid GC content might be a mixed strategy of species to optimize fitness in fluctuating climates, partly through influencing the trade-off between AT → GC and GC → AT mutations.

Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae)

Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R₂ index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272-Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome-wide variation in GC content and is associated with higher methylation levels. Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana

Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selection. Here, using whole-genome, transcriptome, and methylome data from >600 Arabidopsis thaliana individuals, we set out to identify important features influencing selective constraint. Our analyses reveal that multiple factors underlie the accumulation of maladaptive mutations, including gene expression level, gene network connectivity, and gene-body methylation. We then focus on a feature with major effect, nucleotide composition. The ancestral vs. derived status of segregating alleles suggests that GC-biased gene conversion, a recombination-associated process that increases the frequency of G and C nucleotides regardless of their fitness effects, shapes sequence patterns in A. thaliana Through estimation of mutational effects, we present evidence that biased gene conversion hinders the purging of deleterious mutations and contributes to a genome-wide signal of decreased efficacy of selection. By comparing these results to two outcrossing relatives, Arabidopsis lyrata and Capsella grandiflora, we find that protein evolution in A. thaliana is as strongly affected by biased gene conversion as in the outcrossing species. Last, we perform simulations to show that natural levels of outcrossing in A. thaliana are sufficient to facilitate biased gene conversion despite increased homozygosity due to selfing. Together, our results show that even predominantly selfing taxa are susceptible to biased gene conversion, suggesting that it may constitute an important constraint to adaptation among plant species.

A report on DNA sequence determinants in gene expression

The biased usage of nucleotides in coding sequence and its correlation with gene expression has been observed in several studies. A complex set of interactions between genes and other components of the expression system determine the amount of proteins produced from coding sequences. It is known that the elongation rate of polypeptide chain is affected by both codon usage bias and specific amino acid compositional constraints. Therefore, it is of interest to review local DNA-sequence elements and other positional as well as combinatorial constraints that play significant role in gene expression.

A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha

Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule-scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high-density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map-based cloning, feasible.

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

BACKGROUND

Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized.

RESULTS

Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways.

CONCLUSIONS

The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied in a handful of model organisms so far, and can be affected by confounding, nonadaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data, we analyzed the relationship between codon usage, gene expression, allele frequency distribution, and recombination rate in 30 nonmodel species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analyzing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons tend to be preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes

Spiders are an ancient and extremely diverse animal order. They show a considerable diversity of genome sizes, karyotypes and sex chromosomes, which makes them promising models to analyse the evolution of these traits. Our study is focused on the evolution of the genome and chromosomes in haplogyne spiders with holokinetic chromosomes. Although holokinetic chromosomes in spiders were discovered a long time ago, information on their distribution and evolution in these arthropods is very limited. Here we show that holokinetic chromosomes are an autapomorphy of the superfamily Dysderoidea. According to our hypothesis, the karyotype of ancestral Dysderoidea comprised three autosome pairs and a single X chromosome. The subsequent evolution has frequently included inverted meiosis of the sex chromosome and an increase of 2n. We demonstrate that caponiids, a sister clade to Dysderoidea, have enormous genomes and high diploid and sex chromosome numbers. This pattern suggests a polyploid event in the ancestors of caponiids. Holokinetic chromosomes could have arisen by subsequent multiple chromosome fusions and a considerable reduction of the genome size. We propose that spider sex chromosomes probably do not pose a major barrier to polyploidy due to specific mechanisms that promote the integration of sex chromosome copies into the genome.

The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process

Understanding how proteins evolve is important, and the order of amino acids being recruited into the genetic codons was found to be an important factor shaping the amino acid composition of proteins. The latest work about the last universal common ancestor (LUCA) makes it possible to determine the potential factors shaping amino acid compositions during evolution. Those LUCA genes/proteins from Methanococcus maripaludis S2, which is one of the possible LUCA, were investigated. The evolutionary rates of these genes positively correlate with GC contents with P-value significantly lower than 0.05 for 94% homologous genes. Linear regression results showed that compositions of amino acids coded by GC-rich codons positively contribute to the evolutionary rates, while these amino acids tend to be gained in GC-rich organisms according to our results. The first principal component correlates with the GC content very well. The ratios of amino acids of the LUCA proteins coded by GC rich codons positively correlate with the GC content of different bacteria genomes, while the ratios of amino acids coded by AT rich codons negatively correlate with the increase of GC content of genomes. Next, we found that the recruitment order does correlate with the amino acid compositions, but gain and loss in codons showed newly recruited amino acids are not significantly increased along with the evolution. Thus, we conclude that GC content is a primary factor shaping amino acid compositions. GC content shapes amino acid composition to trade off the cost of amino acids with bases, which could be caused by the energy efficiency.

Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species

Population genetic theory predicts that selection should be more effective when the effective population size (N_e) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger N_e. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.

A reference genome of the European beech (Fagus sylvatica L.)

Background

The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.

Findings

Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.

Conclusions

The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.

Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA

Standard Illumina libraries are biased toward sequences of intermediate GC-content. This results in an underrepresentation of GC-rich regions in sequencing projects of genomes with heterogeneous base composition, such as mammals and birds. We developed a simple, cost-effective protocol to enrich sheared genomic DNA in its GC-rich fraction by subtracting AT-rich DNA. This was achieved by heating DNA up to 90 °C before applying Illumina library preparation. We tested the new approach on chicken DNA and found that heated DNA increased average coverage in the GC-richest chromosomes by a factor up to six. Using a Taq polymerase supposedly appropriate for PCR amplification of GC-rich sequences had a much weaker effect. Our protocol should greatly facilitate sequencing and resequencing of the GC-richest regions of heterogeneous genomes, in combination with standard short-read and long-read technologies.

Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants

RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N⁶-methyladenosine (m⁶A) modification tends to have less RNA structure in 3' UTR, whereas GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation. Comparative analysis of RNA structurome between rice and Arabidopsis revealed that higher GC content does not lead to stronger structure and less RNA structural flexibility. Moreover, we found a weak correlation between sequence and structure conservation of the orthologs between rice and Arabidopsis. The conservation and divergence of both sequence and in vivo RNA structure corresponds to diverse and specific biological processes. Our results indicate that RNA secondary structure might offer a separate layer of selection to the sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently in various biological processes to maintain robustness in development and adaptational flexibility during angiosperm evolution.

Codon usage and codon pair patterns in non-grass monocot genomes

BACKGROUND AND AIMS

Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots.

METHODS

First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces.

KEY RESULTS

The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots.

CONCLUSION

Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

BACKGROUND

Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences.

RESULTS

We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol.

CONCLUSIONS

We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits. In this study, we analyzed conserved and divergent root transcriptional responses between flood-tolerant Embrapa 45 and flood-sensitive BR 4 soybean cultivars under hypoxic stress conditions with RNA-seq. To understand how soybean genes evolve and respond to hypoxia, stable and differentially expressed genes were characterized structurally and compositionally comparing its mechanistic relationship. Between cultivars, Embrapa 45 showed less up- and more down-regulated genes, and stronger induction of phosphoglucomutase (Glyma05g34790), unknown protein related to N-terminal protein myristoylation (Glyma06g03430), protein suppressor of phyA-105 (Glyma06g37080), and fibrillin (Glyma10g32620). RNA-seq and qRT-PCR analysis of non-symbiotic hemoglobin (Glyma11g12980) indicated divergence in gene structure between cultivars. Transcriptional changes for genes in amino acids and derivative metabolic process suggest involvement of amino acids metabolism in tRNA modifications, translation accuracy/efficiency, and endoplasmic reticulum stress in both cultivars under hypoxia. Gene groups differed in promoter TATA box, ABREs (ABA-responsive elements), and CRT/DREs (C-repeat/dehydration-responsive elements) frequency. Gene groups also differed in structure, composition, and codon usage, indicating biological significances. Additional data suggests that cis-acting ABRE elements can mediate gene expression independent of ABA in soybean roots under hypoxia.

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces-selection, mutational biases, and GC-biased gene conversion (gBGC)-on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus.

Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens

A long-term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support. Here, we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. Our conclusion is supported by four independent lines of evidence: 1) Very weak or nonsignificant correlation between gene expression and codon usage bias, 2) no increased codon usage bias in more broadly expressed genes, 3) no evidence that codon usage bias would constrain synonymous and nonsynonymous divergence, and 4) predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens.

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

In protein coding genes, base composition strongly varies within and among plant genomes, especially at positions where changes do not alter the coded protein (synonymous variations). Some species, such as the model plant Arabidopsis thaliana, are relatively GC-poor and homogeneous while others, such as grasses, are highly heterogeneous and GC-rich. The causes of these variations are still debated: are they mainly due to selective or neutral processes? Answering to this question is important to correctly infer whether variations in base composition may have functional roles or not. We extended a population genetics method to jointly estimate the different forces that may affect synonymous variations and applied it to genomic datasets in 11 flowering plant species. We found that GC-biased gene conversion, a neutral process associated with recombination that mimics selection by favouring G and C bases, is a widespread and stronger process than selection and that it could explain the large variation in base composition observed in plant genomes. Our results bear implications for analysing plant genomes and for correctly interpreting what could be functional or not.

Towards a whole-genome sequence for rye (Secale cereale L.)

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.

Doubled Haploid 'CUDH2107' as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility

Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line ‘CUDH2107’ by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits.

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus

Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.

Meiotic recombination and genome evolution in plants

Homologous recombination affects genome evolution through crossover, gene conversion and point mutations. Whole genome sequencing together with a detailed epigenome analysis have shed new light on our understanding of how meiotic recombination shapes plant genes and genome structure. Crossover events are associated with DNA sequence motifs, together with an open chromatin signature (hypomethylated CpGs, low nucleosome occupancy or specific histone modifications). The crossover landscape may differ between male and female meiocytes and between species. At the gene level, crossovers occur preferentially in promoter regions in Arabidopsis. In recent years, there is rising support suggesting that biased mismatch repair during meiotic recombination may increase GC content genome-wide and may be responsible for the GC content gradient found in many plant genes.

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

Exonic splice enhancers (ESEs) are short nucleotide motifs, enriched near exon ends, that enhance the recognition of the splice site and thus promote splicing. Are intronless genes under selection to avoid these motifs so as not to attract the splicing machinery to an mRNA that should not be spliced, thereby preventing the production of an aberrant transcript? Consistent with this possibility, we find that ESEs in putative recent retrocopies are at a higher density and evolving faster than those in other intronless genes, suggesting that they are being lost. Moreover, intronless genes are less dense in putative ESEs than intron-containing ones. However, this latter difference is likely due to the skewed base composition of intronless sequences, a skew that is in line with the general GC richness of few exon genes. Indeed, after controlling for such biases, we find that both intronless and intron-containing genes are denser in ESEs than expected by chance. Importantly, nucleotide-controlled analysis of evolutionary rates at synonymous sites in ESEs indicates that the ESEs in intronless genes are under purifying selection in both human and mouse. We conclude that on the loss of introns, some but not all, ESE motifs are lost, the remainder having functions beyond a role in splice promotion. These results have implications for the design of intronless transgenes and for understanding the causes of selection on synonymous sites.

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays

Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC₁, GC₂, and GC₃, collectively termed GC_x) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GC_x bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GC_x genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GC_x genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GC_x genes.

Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes

Plant genomes present a continuous range of variation in nucleotide composition (G + C content). In coding regions, G + C-poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5′–3′ gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5′–3′ decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5′–3′ gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.