Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions

Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus

Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.

Mapping QTLs for 15 morpho-metric traits in Arabidopsis thaliana using Col-0 × Don-0 population

Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F₂ mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.

Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence

Tetep is a rice cultivar known for broad-spectrum resistance to blast, a devastating fungal disease. The molecular basis for its broad-spectrum resistance is still poorly understood. Is it because Tetep has many more NLR genes than other cultivars? Or does Tetep possess multiple major NLR genes that can individually confer broad-spectrum resistance to blast? Moreover, are there many interacting NLR pairs in the Tetep genome? We sequenced its genome, obtained a high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat (NLR) genes. We cloned and tested 219 NLR genes as transgenes in 2 susceptible cultivars using 5 to 12 diversified pathogen strains; in many cases, fewer than 12 strains were successfully cultured for testing. Ninety cloned NLRs showed resistance to 1 or more pathogen strains and each strain was recognized by multiple NLRs. However, few NLRs showed resistance to >6 strains, so multiple NLRs are apparently required for Tetep's broad-spectrum resistance to blast. This was further supported by the pedigree analyses, which suggested a correlation between resistance and the number of Tetep-derived NLRs. In developing a method to identify NLR pairs each of which functions as a unit, we found that >20% of the NLRs in the Tetep and 3 other rice genomes are paired. Finally, we designed an extensive set of molecular markers for rapidly introducing clustered and paired NLRs in the Tetep genome for breeding new resistant cultivars. This study increased our understanding of the genetic basis of broad-spectrum blast resistance in rice.

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.

A gene graveyard in the genome of the fungus Podospora comata

Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories. Comparison of the genome of P. comata with that of P. anserina, whose genome is available for over 10 years, should yield interesting data related to the modalities of genome evolution between these two closely related fungal species that thrive in the same types of biotopes, i.e., herbivore dung. Here, we present the genome sequence of the mat + isolate of the P. comata reference strain T. Comparison with the genome of the mat + isolate of P. anserina strain S confirms that P. anserina and P. comata are likely two different species that rarely interbreed in nature. Despite having a 94-99% of nucleotide identity in the syntenic regions of their genomes, the two species differ by nearly 10% of their gene contents. Comparison of the species-specific gene sets uncovered genes that could be responsible for the known physiological differences between the two species. Finally, we identified 428 and 811 pseudogenes (3.8 and 7.2% of the genes) in P. anserina and P. comata, respectively. Presence of high numbers of pseudogenes supports the notion that difference in gene contents is due to gene loss rather than horizontal gene transfers. We propose that the high frequency of pseudogenization leading to gene loss in P. anserina and P. comata accompanies specialization of these two fungi. Gene loss may be more prevalent during the evolution of other fungi than usually thought.

The pseudogenes of barley

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.

Comprehensive analysis of NAC transcription factors and their expression during fruit spine development in cucumber (Cucumis sativus L.)

The cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and fruit trichomes or spines are an important trait for external fruit quality. The mechanisms underlying spine formation are not well understood, but the plant-specific NAC family of transcription factors may play important roles in fruit spine initiation and development. In this study, we conducted a genome-wide survey and identified 91 NAC gene homologs in the cucumber genome. Clustering analysis classified these genes into six subfamilies; each contained a varying number of NAC family members with a similar intron-exon structure and conserved motifs. Quantitative real-time PCR analysis revealed tissue-specific expression patterns of these genes, including 10 and 12 that exhibited preferential expression in the stem and fruit, respectively. Thirteen of the 91 NAC genes showed higher expression in the wild-type plant than in its near-isogenic trichome mutant, suggesting their important roles in fruit spine development. Exogenous application of four plant hormones promoted spine formation and increased spine density on the cucumber fruits; several NAC genes showed differential expression over time in response to phytohormone treatments on cucumber fruit, implying their essential roles in fruit-trichome development. Among the NAC genes identified, 12 were found to be targets of 13 known cucumber micro-RNAs. Collectively, these findings provide a useful resource for further analysis of the interactions between NAC genes and genes underlying trichome organogenesis and development during fruit spine development in cucumber.

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences

A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.

Non-canonical structure, function and phylogeny of the Bsister MADS-box gene OsMADS30 of rice (Oryza sativa)

Bsister MADS-box genes play key roles in female reproductive organ and seed development throughout seed plants. This view is supported by their high conservation in terms of sequence, expression and function. In grasses, there are three subclades of Bsister genes: the OsMADS29-, the OsMADS30- and the OsMADS31-like genes. Here, we report on the evolution of the OsMADS30-like genes. Our analyses indicate that these genes evolved under relaxed purifying selection and are rather weakly expressed. OsMADS30, the representative of the OsMADS30-like genes from rice (Oryza sativa), shows strong sequence deviations in its 3' region when compared to orthologues from other grass species. We show that this is due to a 2.4-kbp insertion, possibly of a hitherto unknown helitron, which confers a heterologous C-terminal domain to OsMADS30. This putative helitron is not present in the OsMADS30 orthologues from closely related wild rice species, pointing to a relatively recent insertion event. Unlike other Bsister mutants O. sativa plants carrying a T-DNA insertion in the OsMADS30 gene do not show aberrant seed phenotypes, indicating that OsMADS30 likely does not have a canonical 'Bsister function'. However, imaging-based phenotyping of the T-DNA carrying plants revealed alterations in shoot size and architecture. We hypothesize that sequence deviations that accumulated during a period of relaxed selection in the gene lineage that led to OsMADS30 and the alteration of the C-terminal domain might have been a precondition for a potential neo-functionalization of OsMADS30 in O. sativa.

High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae

Background

Three NBS-LRR genes, Rpi-blb2, Mi-1.2, and Cami, constitute a very special plant resistance gene family. These genes confer resistance against 4 distantly related pathogen species in 3 different Solanaceae hosts. To characterize this noted resistance, we conducted a series of studies on this gene family.

Results

First, homologs of this gene family were identified in the pepper, tomato and potato genomes. This revealed a large variation in copy number within this gene family among species and a great divergence was found both between and within species. To gain more information pertaining to gene resistance within this family, 121 LRR regions were cloned in 16 different wild/cultivated potato accessions. Again, frequent copy number variations and a high level of divergence between homolog were observed common among accessions. The divergence within species was so high that it reaches the level of divergence between species. Also, frequent frameshift mutations and abundant gene conversion events were identified in these LRR regions.

Conclusions

Our findings suggest that this family harbors an unusually high level of genetic abundance, making it of particular interest. Together with other reported examples, our study also provides evidence that multi-resistance is a common trait in R gene families like this.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0493-z) contains supplementary material, which is available to authorized users.

Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana

Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence, and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus, it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here, we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 (DDF1) and DDF2, that duplicated through paleopolyploidy 50 to 65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of Arabidopsis thaliana (At)DDF1 and AtDDF2 have diverged in a highly asymmetric manner, and AtDDF2 has lost most inferred ancestral stress responses. Consistent with promoter disablement, the AtDDF2 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of AtDDF1, AtDDF2, and their Arabidopsis lyrata orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an AtDDF2-specific substitution within the DNA-binding domain significantly reduces binding affinity. Cross-species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint, but among A. thaliana accessions, AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1. This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication.

GENCODE pseudogenes

Historically pseudogenes were believed to represent nonfunctional genomic fossils; however, there is emerging evidence that many of them could be biologically active. This possibility has ignited interest in pseudogene loci and made the need for their high-quality annotation more pressing as an accurate knowledge of all pseudogenes in the human reference genome sequence facilitates confident functional analysis. GENCODE have undertaken the first genome-wide pseudogene assignment for protein-coding genes combining both large-scale manual annotation and computational pseudogene prediction pipelines. Multiple computational predictions provide an unbiased set of hints for manual annotators to investigate, both during first-pass annotation and as part of QC to identify any potential missing pseudogene loci. Where a pseudogene is identified, the extent of its homology to the parent locus is fully investigated by a manual annotator; a pseudogene model is built and assigned to one of eight pseudogene biotypes depending on the mechanism of creation and on the presence of locus-specific transcriptional or proteomic data. The high-quality, information-rich set of pseudogenes created has been integrated with ENCODE functional genomics data, specifically expression level, transcription factor and RNA polymerase II binding, and chromatin marks. In this way we have been able to identify some pseudogenes that possess conventional characteristics of functionality as well as others with interesting patterns of partial activity, which might suggest that putatively inactive loci could be gaining a novel function, for example as long noncoding RNAs. The activity data associated with every pseudogene is stored in the psiDR resource.

Functional requirements driving the gene duplication in 12 Drosophila species

BACKGROUND

Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue.

RESULTS

In our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses.

CONCLUSIONS

This study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila.