Duplicate Pairs Research Articles

Genome-wide identification and evolutionary analysis of neutral/alkaline invertases in Brassica rapa

Among the several sucrose-catabolizing enzymes, neutral/alkaline invertases (NINs) play crucial roles in developmental processes as well as environmental stress responses in higher plants. Despite the fact that NINs are essential enzymes for plant life, the NIN family and their evolutionary relationships are poorly understood. Therefore, in this study, we identified 11 NINs in the Brassica rapa (Chinese cabbage; BraNINs) genome, and analyzed the evolutionary mechanisms of BraNIN genes. Evolution analysis suggested that the BraNIN genes were duplicated via a segmental duplication event originating 15.81–45.25 million years ago. Furthermore, two segmental duplicated pairs (BraNIN5/6 and BraNIN7/8) were subject to negative selection. Furthermore, expression analysis of BraNINs using RNA-sequencing data suggested various functions of BraNINs during responses to drought stress. Taken together, our comparative genomic analysis of NIN genes in B. rapa provides information that will assist future studies on sucrose metabolism in sinks and sources of higher plants.

Genetic analysis of a heritage variety collection

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Comparative Genomic and Transcriptomic Analyses of Family-1 UDP Glycosyltransferase in Prunus Mume.

Glycosylation mediated by Family-1 UDP-glycosyltransferases (UGTs) plays crucial roles in plant growth and adaptation to various stress conditions. Prunus mume is an ideal crop for analyzing flowering for its early spring flowering characteristics. Revealing the genomic and transcriptomic portfolio of the UGT family in P. mume, a species in which UGTs have not yet been investigated, is therefore important. In this study, 130 putative UGT genes were identified and phylogenetically clustered into 14 groups. These PmUGTs were distributed unevenly across eight chromosomes and 32 tandem duplication and 8 segmental duplication pairs were revealed. A highly conserved intron insertion event was revealed on the basis of intron/exon patterns within PmUGTs. According to RNA-seq data, these PmUGTs were specifically expressed in different tissues and during the bud dormancy process. In addition, we confirmed the differential expression of some representative genes in response to abscisic acid treatment. Our results will provide important information on the UGT family in P. mume that should aid further characterization of their biological roles in response to environmental stress.

Function of the evolutionarily conserved plant methionine-S-sulfoxide reductase without thecatalytic residue.

In plants, two types of methionine sulfoxide reductase (MSR) exist, namely methionine-S-sulfoxide reductase (MSRA) and methionine-R-sulfoxide reductase (MSRB). These enzymes catalyze the reduction of methionine sulfoxides (MetO) back to methionine (Met) by a catalytic cysteine (Cys) and one or two resolving Cys residues. Interestingly, a group of MSRA encoded by plant genomes does not have a catalytic residue. We asked that if this group of MSRA did not have any function (as fitness), why it was not lost during the evolutionary process. To challenge this question, we analyzed the gene family encoding MSRA in soybean (GmMSRAs). We found seven genes encoding GmMSRAs, which included three segmental duplicated pairs. Among them, a pair of duplicated genes, namely GmMSRA1 and GmMSRA6, was without a catalytic Cys residue. Pseudogenes were ruled out astheir transcripts were detected in various tissues and their Ka/Ks ratio indicated a negative selection pressure. In vivo analysis in Δ3MSR yeast strain indicated that the GmMSRA6 did not have activity toward MetO, contrasting to GmMSRA3 which had catalytic Cys and had activity. When exposed to H2O2-induced oxidative stress, GmMSRA6 did not confer any protection to the Δ3MSR yeast strain. Overexpression of GmMSRA6 in Arabidopsis thaliana did not alter the plant's phenotype under physiological conditions. However, the transgenic plants exhibited slightly higher sensitivity toward salinity-induced stress. Taken together, this data suggested that the plant MSRAs withoutthe catalytic Cys are not enzymatically active and their existence may be explained by a role in regulating plant MSR activity via dominant-negative substrate competition mechanism.

Diversification of SQUAMOSA promoter binding protein-like (SPL) genes by changes of miR156/529 binding sites in land plants

Gene duplication can increase functional diversity of a gene family. SQUAMOSA promoter binding protein-like (SPL) genes encode plant-specific transcription factors. The SPL genes are regulated by miR156 and miR529 microRNA families. However, little is known about how and if duplicated SPL genes (paralogs) have retained active miR156/529 binding sites. Here, we analyzed 136 SPL genes from eight representative land plants, in which 70 of them originated from several large-scale duplication events, 40 ones constituted 32 duplicated target pairs. In this study, these target pairs were divided into divergent pattern (D-type) and same pattern (S-type). The D-pattern included loss/gain of miRNA binding sites on one paralog (D-1) and the mutation on miRNA binding sequences (D-2). Further study indicated that D-type gene pairs had the higher sequence divergence and evolutionary rate than S-type ones. Meanwhile, D-type gene pairs exhibited the different expression patterns, whereas S-type gene pairs had the similar expression patterns. These results revealed that the different divergence of miR156/529 binding sites after gene duplication might contribute to increasing functional diversity of SPL genes. In addition, gene structural analysis suggested that exonization/pseudoexonization and indel were two main mechanisms to gain/loss and shift the miR156/529 binding sites after gene duplications, and the latter might easily introduce the mutation when miRNA binding sites shifted from the coding region to untranslated region. Therefore, this study provides the better understanding the functional diversity of SPL genes in land plants.

Pinning down ploidy in paleopolyploid plants

BackgroundFractionation is the genome-wide process of losing one gene per duplicate pair following whole genome multiplication (doubling, tripling, …). This is important in the evolution of plants over tens of millions of years, because of their repeated cycles of genome multiplication and fractionation. One type of evidence in the study of these processes is the frequency distribution of similarities between the two genes, over all the duplicate pairs in the genome.ResultsWe study modeling and inference problems around the processes of fractionation and whole genome multiplication focusing first on the frequency distribution of similarities of duplicate pairs in the genome. Our birth-and-death model accounts for repeated duplication, triplication or other multiplication events, as well as fractionation rates among multiple progeny of a single gene specific to each event. It also has a biologically and combinatorially well-motivated way of handling the tendency for at least one sibling to survive fractionation. The method settles previously unexplored questions about the expected number of gene pairs tracing their ancestry back to each multiplication event. We exemplify the algebraic concepts inherent in our models and on Brassica rapa, whose evolutionary history is well-known. We demonstrate the quantitative analysis of high-similarity gene pairs and triples to confirm the known ploidies of events in the lineage of B. rapa.ConclusionsOur birth-and-death model accounts for the similarity distribution of paralogs in terms of multiple rounds of whole genome multiplication and fractionation. An analysis of high-similarity gene triples confirms the recent Brassica triplication.

Genome-wide identification of the auxin response factor gene family in Cicer arietinum

BackgroundAuxin Response Factors act as critical components of the auxin-signaling pathway by regulating the transcription of auxin-responsive genes. The release of the chickpea reference genome provides an opportunity to identify and characterize the ARF gene family in this important legume by a data mining coupled by comparative genomics approaches.ResultsWe performed a comprehensive characterization and analysis of 24 ARF genes in the chickpea reference genome. Comparative phylogenetic analysis of the ARF from chickpea, Medicago and Arabidopsis suggests that recent duplications have played a very limited role in the expansion of the ARF chickpea family. Gene structure analysis based on exon-intron organization provides additional evidence to support the evolutionary relationship among the ARF members. Conserved motif analysis shows that most of the proteins fit into the canonical ARF structure model, but 9 proteins lack or have a truncated dimerization domain. The mechanisms underlying the diversification of the ARF gene family are based on duplications, variations in domain organization and alternative splicing. Concerning duplications, segmental, but not tandem duplications, have contributed to the expansion of the gene family. Moreover, the duplicated pair genes have evolved mainly under the influence of purifying selection pressure with restricted functional divergence. Expression profiles responding to various environmental stimuli show a close relationship between tissue and expression patterns. Promoter sequence analysis reveals an enrichment of several cis-regulatory elements related to symbiosis, and modulation of plant gene expression during the interaction with microbes.ConclusionsIn conclusion, this study provides a comprehensive overview of the ARF gene family in chickpea. Globally, our data supports that auxin signaling pathway regulates a wide range of physiological processes and stress responses. Our findings could further provide new insights into the complexity of the regulation of ARF at the transcription level that may be useful to develop rational chickpea breeding strategies to improve development or stress responses. Our study also provides a foundation for comparative genomic analyses and a framework to trace the dynamic evolution of ARF genes on a large time-scale within the legume family.

MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution.

The repertoire of miRNAs has considerably expanded during metazoan evolution, and duplication is an important mechanism for generating new functional miRNAs. However, relatively little is known about the functional divergence between paralogous miRNAs and the possible coevolution between duplicated miRNAs and the genomic contexts. By systematically examining small RNA expression profiles across various human tissues and interrogating the publicly available miRNA:mRNA pairing chimeras, we found that changes in expression patterns and targeting preferences are widespread for duplicated miRNAs in vertebrates. Both the empirical interactions and target predictions suggest that evolutionarily conserved homo-seed duplicated miRNAs pair with significantly higher numbers of target sites compared to the single-copy miRNAs. Our birth-and-death evolutionary analysis revealed that the new target sites of miRNAs experienced frequent gains and losses during function development. Our results suggest that a newly emerged target site has a higher probability to be functional and maintained by natural selection if it is paired to a seed shared by multiple paralogous miRNAs rather than being paired to a single-copy miRNA. We experimentally verified the divergence in target repression between two paralogous miRNAs by transfecting let-7a and let-7b mimics into kidney-derived cell lines of four mammalian species and measuring the resulting transcriptome alterations by extensive high-throughput sequencing. Our results also suggest that the gains and losses of let-7 target sites might be associated with the evolution of repressiveness of let-7 across mammalian species.

Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid

BackgroundPolyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization.ResultsWe compared the genome sequences of tetraploid cotton (Gossypium hirsutum) and its two diploid progenitors, G. arboreum and G. raimondii, and found that the bHLH genes were conserved over the polyploidization. Oppositely, the expression of the homeolgous gene pairs was diversified. The biased homeologous proportion for bHLH family is significantly higher (64.6%) than the genome wide homeologous expression bias (40%). Compared with cacao (T. cacao), orthologous genes only accounted for a small proportion (41.7%) of whole cotton bHLHs family. The further Ks analysis indicated that bHLH genes underwent at least two distinct episodes of whole genome duplication: a recent duplication (1.0–60.0 million years ago, MYA, 0.005 < Ks < 0.312) and an old duplication (> 60.0 MYA, 0.312 < Ks < 3.0). The old duplication event might have played a key role in the expansion of the bHLH family. Both recent and old duplicated pairs (68.8%) showed a divergent expression profile, indicating specialized functions. The expression diversification of the duplicated genes suggested it might be a universal feature of the long-term evolution of cotton.ConclusionsOverview of cotton bHLH proteins indicated a conserved and divergent evolution from diploids to allotetraploid. Our results provided an excellent example for studying the long-term evolution of polyploidy.

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

Most plants are polyploid due to whole-genome duplications (WGD) and can thus have duplicated genes. Following a WGD, paralogs are often fractionated (lost) and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high-resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of genetic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit particular genomic features as they are often associated with proximal transposable elements (TEs) and are preferentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms

Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode. We focus on secretomes of the fungus, which play important roles in pathogenicity and fungus-host/environment interactions, and identified 1,750 secreted proteins, with a high proportion of carboxypeptidases, subtilisins, and chitinases. We analyzed the phylogenies of these genes and predicted new pathogenic molecules. By comparative transcriptome analysis, we found that secreted proteins involved in responses to nutrient stress are mainly comprised of proteases and glycoside hydrolases. Moreover, 32 secreted proteins undergoing positive selection and 71 duplicated gene pairs encoding secreted proteins are identified. Two duplicated pairs encoding secreted glycosyl hydrolases (GH30), which may be related to fungal endophytic process and lost in many insect-pathogenic fungi but exist in nematophagous fungi, are putatively acquired from bacteria by horizontal gene transfer. The results help understanding genetic origins and evolution of parasitism-related genes.

Causes of blood methylomic variation for middle-aged women measured by the HumanMethylation450 array

ABSTRACTTo address the limitations in current classic twin/family research on the genetic and/or environmental causes of human methylomic variation, we measured blood DNA methylation for 479 women (mean age 56 years) including 66 monozygotic (MZ), 66 dizygotic (DZ) twin pairs and 215 sisters of twins, and 11 random technical duplicates using the HumanMethylation450 array. For each methylation site, we estimated the correlation for pairs of duplicates, MZ twins, DZ twins, and siblings, fitted variance component models by assuming the variation is explained by genetic factors, by shared and individual environmental factors, and by independent measurement error, and assessed the best fitting model. We found that the average (standard deviation) correlations for duplicate, MZ, DZ, and sibling pairs were 0.10 (0.35), 0.07 (0.21), -0.01 (0.14) and -0.04 (0.07). At the genome-wide significance level of 10−7, 93.3% of sites had no familial correlation, and 5.6%, 0.1%, and 0.2% of sites were correlated for MZ, DZ, and sibling pairs. For 86.4%, 6.9%, and 7.1% of sites, the best fitting model included measurement error only, a genetic component, and at least one environmental component. For the 13.6% of sites influenced by genetic and/or environmental factors, the average proportion of variance explained by environmental factors was greater than that explained by genetic factors (0.41 vs. 0.37, P value <10−15). Our results are consistent with, for middle-aged woman, blood methylomic variation measured by the HumanMethylation450 array being largely explained by measurement error, and more influenced by environmental factors than by genetic factors.

Quickly identifying identical and closely related subjects in large databases using genotype data.

Genome-wide association studies (GWAS) usually rely on the assumption that different samples are not from closely related individuals. Detection of duplicates and close relatives becomes more difficult both statistically and computationally when one wants to combine datasets that may have been genotyped on different platforms. The dbGaP repository at the National Center of Biotechnology Information (NCBI) contains datasets from hundreds of studies with over one million samples. There are many duplicates and closely related individuals both within and across studies from different submitters. Relationships between studies cannot always be identified by the submitters of individual datasets. To aid in curation of dbGaP, we developed a rapid statistical method called Genetic Relationship and Fingerprinting (GRAF) to detect duplicates and closely related samples, even when the sets of genotyped markers differ and the DNA strand orientations are unknown. GRAF extracts genotypes of 10,000 informative and independent SNPs from genotype datasets obtained using different methods, and implements quick algorithms that enable it to find all of the duplicate pairs from more than 880,000 samples within and across dbGaP studies in less than two hours. In addition, GRAF uses two statistical metrics called All Genotype Mismatch Rate (AGMR) and Homozygous Genotype Mismatch Rate (HGMR) to determine subject relationships directly from the observed genotypes, without estimating probabilities of identity by descent (IBD), or kinship coefficients, and compares the predicted relationships with those reported in the pedigree files. We implemented GRAF in a freely available C++ program of the same name. In this paper, we describe the methods in GRAF and validate the usage of GRAF on samples from the dbGaP repository. Other scientists can use GRAF on their own samples and in combination with samples downloaded from dbGaP.

Effective estimation of the minimum number of amino acid residues required for functional divergence between duplicate genes

One of hot research foci has always been predicting amino acid residues underlying functional divergence after gene duplication, as those predicted sites can be used as candidates for further functional experimentations. It is important and interesting to know how many sites, on average, may have been responsible for the functional divergence between duplicate genes. In this article, we studied two basic types of functional divergence (type-I and type-II) in depth in order to give an accurate estimation of functional divergence-related sites. Type-I divergences result from altered functional constraints (i.e., different evolutionary rates) between duplicate genes, whereas type-II divergences refer to residues that are conserved by functional constraints but exhibit different physicochemical properties (e.g., charge or hydrophobicity) between duplicates. An effective site number (NE) strategy was applied in our study, which implements a stepwise regression model to calculate the minimum number of residues responsible for functional divergence without choosing preset threshold. We found that NE-determined cut-off value varies among different duplicate pairs, suggesting that empirical cutoff value is not suitable for every case. Under our standard NE calculation method, we estimated less than 15% of residues that are required for paralogous gene functional divergence. Finally, we established a database, DIVERGE-D, as a public resource for the predicted NE sites between two paralogs in this study, which can be used as candidates for further biological engineering and experimentation.

Using Probabilistic Record Linkage of Structured and Unstructured Data to Identify Duplicate Cases in Spontaneous Adverse Event Reporting Systems.

Duplicate case reports in spontaneous adverse event reporting systems pose a challenge for medical reviewers to efficiently perform individual and aggregate safety analyses. Duplicate cases can bias data mining by generating spurious signals of disproportional reporting of product-adverse event pairs. We have developed a probabilistic record linkage algorithm for identifying duplicate cases in the US Vaccine Adverse Event Reporting System (VAERS) and the US Food and Drug Administration Adverse Event Reporting System (FAERS). In addition to using structured field data, the algorithm incorporates the non-structured narrative text of adverse event reports by examining clinical and temporal information extracted by the Event-based Text-mining of Health Electronic Records system, a natural language processing tool. The final component of the algorithm is a novel duplicate confidence value that is calculated by a rule-based empirical approach that looks for similarities in a number of criteria between two case reports. For VAERS, the algorithm identified 77% of known duplicate pairs with a precision (or positive predictive value) of 95%. For FAERS, it identified 13% of known duplicate pairs with a precision of 100%. The textual information did not improve the algorithm's automated classification for VAERS or FAERS. The empirical duplicate confidence value increased performance on both VAERS and FAERS, mainly by reducing the occurrence of false-positives. The algorithm was shown to be effective at identifying pre-linked duplicate VAERS reports. The narrative text was not shown to be a key component in the automated detection evaluation; however, it is essential for supporting the semi-automated approach that is likely to be deployed at the Food and Drug Administration, where medical reviewers will perform some manual review of the most highly ranked reports identified by the algorithm.

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

BackgroundGene duplication has been identified as a key process driving functional change in many genomes. Several biological models exist for the evolution of a pair of duplicates after a duplication event, and it is believed that gene duplicates can evolve in different ways, according to one process, or a mix of processes. Subfunctionalization is one such process, under which the two duplicates can be preserved by dividing up the function of the original gene between them. Analysis of genomic data using subfunctionalization and related processes has thus far been relatively coarse-grained, with mathematical treatments usually focusing on the phenomenological features of gene duplicate evolution.ResultsHere, we develop and analyze a mathematical model using the mechanics of subfunctionalization and the assumption of Poisson rates of mutation. By making use of the results from the literature on the Phase-Type distribution, we are able to derive exact analytical results for the model.The main advantage of the mechanistic model is that it leads to testable predictions of the phenomenological behavior (instead of building this behavior into the model a priori), and allows for the estimation of biologically meaningful parameters. We fit the survival function implied by this model to real genome data (Homo sapiens, Mus musculus, Rattus norvegicus and Canis familiaris), and compare the fit against commonly used phenomenological survival functions. We estimate the number of regulatory regions, and rates of mutation (relative to silent site mutation) in the coding and regulatory regions.We find that for the four genomes tested the subfunctionalization model predicts that duplicates most-likely have just a few regulatory regions, and the rate of mutation in the coding region is around 5-10 times greater than the rate in the regulatory regions. This is the first model-based estimate of the number of regulatory regions in duplicates.ConclusionsStrong agreement between empirical results and the predictions of our model suggest that subfunctionalization provides a consistent explanation for the evolution of many gene duplicates.

Benchmarks for measurement of duplicate detection methods in nucleotide databases.

: https://bitbucket.org/biodbqual/benchmarks.

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC—a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases.Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w

Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish.

The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.

Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.).

BackgroundMitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes.ResultsIn this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively. Then, chromosome localization, gene structure and conserved protein motifs and phylogenetic relationship as well as regulatory network of these TaMAPKKKs were systematically investigated and results supported the prediction. Furthermore, a total of 11 homologous groups between A, B and D sub-genome and 24 duplication pairs among them were detected, which contributed to the expansion of wheat MAPKKK gene family. Finally, the expression profiles of these MAPKKKs during development and under different abiotic stresses were investigated using the RNA-seq data. Additionally, 10 tissue-specific and 4 salt-responsive TaMAPKKK genes were selected to validate their expression level through qRT-PCR analysis.ConclusionsThis study for the first time reported the genome organization, evolutionary features and expression profiles of the wheat MAPKKK gene family, which laid the foundation for further functional analysis of wheat MAPKKK genes, and contributed to better understanding the roles and regulatory mechanism of MAPKKKs in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2993-7) contains supplementary material, which is available to authorized users.