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author:("Yang, sinai")
1.  Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee 
Genome Biology  2015;16(1):15.
Social hymenoptera, the honey bee (Apis mellifera) in particular, have ultra-high crossover rates and a large degree of intra-genomic variation in crossover rates. Aligned with haploid genomics of males, this makes them a potential model for examining the causes and consequences of crossing over. To address why social insects have such high crossing-over rates and the consequences of this, we constructed a high-resolution recombination atlas by sequencing 55 individuals from three colonies with an average marker density of 314 bp/marker.
We find crossing over to be especially high in proximity to genes upregulated in worker brains, but see no evidence for a coupling with immune-related functioning. We detect only a low rate of non-crossover gene conversion, contrary to current evidence. This is in striking contrast to the ultrahigh crossing-over rate, almost double that previously estimated from lower resolution data. We robustly recover the predicted intragenomic correlations between crossing over and both population level diversity and GC content, which could be best explained as indirect and direct consequences of crossing over, respectively.
Our data are consistent with the view that diversification of worker behavior, but not immune function, is a driver of the high crossing-over rate in bees. While we see both high diversity and high GC content associated with high crossing-over rates, our estimate of the low non-crossover rate demonstrates that high non-crossover rates are not a necessary consequence of high recombination rates.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0566-0) contains supplementary material, which is available to authorized users.
PMCID: PMC4305242  PMID: 25651211
2.  Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae 
BMC Genetics  2014;15:45.
Rice blast fungus Magnaporthe oryzae is one of the most devastating pathogens in rice. Avirulence genes in this fungus share a gene-for-gene relationship with the resistance genes in its host rice. Although numerous studies have shown that rice blast R-genes are extremely diverse and evolve rapidly in their host populations, little is known about the evolutionary patterns of the Avr-genes in the pathogens.
Here, six well-characterized Avr-genes and seven randomly selected non-Avr control genes were used to investigate the genetic variations in 62 rice blast strains from different parts of China. Frequent presence/absence polymorphisms, high levels of nucleotide variation (~10-fold higher than non-Avr genes), high non-synonymous to synonymous substitution ratios, and frequent shared non-synonymous substitution were observed in the Avr-genes of these diversified blast strains. In addition, most Avr-genes are closely associated with diverse repeated sequences, which may partially explain the frequent presence/absence polymorphisms in Avr-genes.
The frequent deletion and gain of Avr-genes and rapid non-synonymous variations might be the primary mechanisms underlying rapid adaptive evolution of pathogens toward virulence to their host plants, and these features can be used as the indicators for identifying additional Avr-genes. The high number of nucleotide polymorphisms among Avr-gene alleles could also be used to distinguish genetic groups among different strains.
PMCID: PMC4021558  PMID: 24725999
Magnaporthe oryzae; Avr-genes; Evolutionary features; Rapid evolution
3.  Packing of Isophthalate Tetracarboxylic Acids on Au(111): Rows and Disordered Herringbone Structures 
Scanning tunnelling microscopy (STM) has been used to investigate the formation of hydrogen-bonded structures of the isophthalate tetracarboxylic acids, biphenyl-3,3′,5,5′-tetracarboxylic acid (BPTC), terphenyl-3,3″,5,5″-tetracarboxylic acid (TPTC), and quarterphenyl-3,3‴,5,5‴-tetracarboxylic acid (QPTC), via deposition from solution onto Au(111). STM data reveal that ordered structures can be formed from an aqueous solution leading to the formation of rows for the shortest acid BPTC, while the longer molecules TPTC and QPTC adopt a herringbone-like structure with significant degrees of disorder. The influence of solvent and substrate on the molecular ordering is discussed, and density functional theory is used to identify molecular models for these new phases.
PMCID: PMC3806148  PMID: 24163714
4.  Functional requirements driving the gene duplication in 12 Drosophila species 
BMC Genomics  2013;14:555.
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.
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.
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.
PMCID: PMC3751352  PMID: 23945147
Young duplication; Environmental factor; Convergent evolution; Adaptive evolution
5.  Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions 
PLoS ONE  2012;7(12):e51769.
Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ∼28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.
PMCID: PMC3521719  PMID: 23272162
6.  Heterogeneous evolutionary rates of Pi2/9 homologs in rice 
BMC Genetics  2012;13:73.
The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome. Although three functional R-genes have been cloned from this locus, little is known about the origin and evolutionary history of these genes. Herein, an extensive genome-wide survey of Pi2/9 homologs in rice, sorghum, Brachypodium and Arabidopsis, was conducted to explore this theme.
In our study, 1, 1, 5 and 156 Pi2/9 homologs were detected in Arabidopsis, Brachypodium, sorghum and rice genomes, respectively. Two distinct evolutionary patterns of Pi2/9 homologs, Type I and Type II, were observed in rice lines. Type I Pi2/9 homologs showed evidence of rapid gene diversification, including substantial copy number variations, obscured orthologous relationships, high levels of nucleotide diversity or/and divergence, frequent sequence exchanges and strong positive selection, whereas Type II Pi2/9 homologs exhibited a fairly slow evolutionary rate. Interestingly, the three cloned R-genes from the Pi2/9 locus all belonged to the Type I genes.
Our data show that the Pi2/9 locus had an ancient origin predating the common ancestor of gramineous species. The existence of two types of Pi2/9 homologs suggest that diversifying evolution should be an important strategy of rice to cope with different types of pathogens. The relationship of cloned Pi2/9 genes and Type I genes also suggests that rapid gene diversification might facilitate rice to adapt quickly to the changing spectrum of the fungal pathogen M. grisea. Based on these criteria, other potential candidate genes that might confer novel resistance specificities to rice blast could be predicted.
PMCID: PMC3492116  PMID: 22900499
Pi2/9; Type I and Type II R-genes; Nucleotide diversity; Copy number variation; Positive selection; Gene conversion
7.  Variation of presence/absence genes among Arabidopsis populations 
Gene presence/absence (P/A) polymorphisms are commonly observed in plants and are important in individual adaptation and species differentiation. Detecting their abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms in a given species. The recently sequenced 80 Arabidopsis genomes provide an opportunity to address these questions.
By systematically investigating these accessions, we identified 2,407 P/A genes (or 8.9%) absent in one or more genomes, averaging 444 absent genes per accession. 50.6% of P/A genes belonged to multi-copy gene families, or 31.0% to clustered genes. However, the highest proportion of P/A genes, outnumbered in singleton genes, was observed in the regions near centromeres. In addition, a significant correlation was observed between the P/A gene frequency among the 80 accessions and the diversity level at P/A loci. Furthermore, the proportion of P/A genes was different among functional gene categories. Finally, a P/A gene tree showed a diversified population structure in the worldwide Arabidopsis accessions.
An estimate of P/A genes and their frequency distribution in the worldwide Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes, by which individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.
PMCID: PMC3433342  PMID: 22697058
8.  Genome-wide investigation reveals high evolutionary rates in annual model plants 
BMC Plant Biology  2010;10:242.
Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.
According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.
The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.
PMCID: PMC3095324  PMID: 21062446
9.  Patterns of exon-intron architecture variation of genes in eukaryotic genomes 
BMC Genomics  2009;10:47.
The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons and introns.
We investigated the length, GC content, ordinal position and divergence in both exons and introns of 13 eukaryotic genomes, representing plant and animal. Our analyses revealed that three basic patterns of exon-intron variation were present in nearly all analyzed genomes (P < 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased. In addition, we observed that the shorter introns had either low or high GC content, and the GC content of long introns was intermediate.
Although the factors contributing to these patterns have not been identified, our results provide three important clues: common factor(s) exist and may shape both exons and introns; the ordinal reduction patterns may reflect a time-orderly evolution; and the larger first and last exons may be splicing-required. These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures.
PMCID: PMC2636830  PMID: 19166620
10.  Highly asymmetric rice genomes 
BMC Genomics  2007;8:154.
Individuals in the same species are assumed to share the same genomic set. However, it is not unusual to find an orthologous gene only in small subset of the species, and recent genomic studies suggest that structural rearrangements are very frequent between genomes in the same species. Two recently sequenced rice genomes Oryza sativa L. var. Nipponbare and O. sativa L. var. 93-11 provide an opportunity to systematically investigate the extent of the gene repertoire polymorphism, even though the genomic data of 93-11 derived from whole-short-gun sequencing is not yet as complete as that of Nipponbare.
We compared gene contents and the genomic locations between two rice genomes. Our conservative estimates suggest that at least 10% of the genes in the genomes were either under presence/absence polymorphism (5.2%) or asymmetrically located between genomes (4.7%). The proportion of these "asymmetric genes" varied largely among gene groups, in which disease resistance (R) genes and the RLK kinase gene group had 11.6 and 7.8 times higher proportion of asymmetric genes than housekeeping genes (Myb and MADS). The significant difference in the proportion of asymmetric genes among gene groups suggests that natural selection is responsible for maintaining genomic asymmetry. On the other hand, the nucleotide diversity in 17 R genes under presence/absence polymorphism was generally low (average nucleotide diversity = 0.0051).
The genomic symmetry was disrupted by 10% of asymmetric genes, which could cause genetic variation through more unequal crossing over, because these genes had no allelic counterparts to pair and then they were free to pair with homologues at non-allelic loci, during meiosis in heterozygotes. It might be a consequence of diversifying selection that increased the structural divergence among genomes, and of purifying selection that decreased nucleotide divergence in each R gene locus.
PMCID: PMC1914357  PMID: 17555605
11.  A Robust Binary Supramolecular Organic Framework (SOF) with High CO2 Adsorption and Selectivity 
Journal of the American Chemical Society  2014;136(37):12828-12831.
A robust binary hydrogen-bonded supramolecular organic framework (SOF-7) has been synthesized by solvothermal reaction of 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)benzene (1) and 5,5′-bis-(azanediyl)-oxalyl-diisophthalic acid (2). Single crystal X-ray diffraction analysis shows that SOF-7 comprises 2 and 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene (3); the latter formed in situ from the oxidative dehydrogenation of 1. SOF-7 shows a three-dimensional four-fold interpenetrated structure with complementary O–H···N hydrogen bonds to form channels that are decorated with cyano and amide groups. SOF-7 exhibits excellent thermal stability and solvent and moisture durability as well as permanent porosity. The activated desolvated material SOF-7a shows high CO2 adsorption capacity and selectivity compared with other porous organic materials assembled solely through hydrogen bonding.
PMCID: PMC4183619  PMID: 25184689

Results 1-11 (11)