My fundamental research aims at understanding genome evolution and biodiversity, impacting agricultural sustainability and ensuring food security. We focus around crop plants and farm animals at DNA, chromosome and genome levels. We use microscopy, bioinformatics, in situ hybridization, molecular genetics, and systems biology to gain a comprehensive understanding of fundamental processes related to chromosomes, polyploidy, and DNA sequence evolution. We evaluate the environmental outcomes of agricultural practices and assess their consequences, including their economic and social impacts. Leveraging the insights from our research allows improved agricultural genetics. I am also involved in research evaluation and teaching.
This paper is concerned with validating a mathematical model of regulation in the tryptophan oper... more This paper is concerned with validating a mathematical model of regulation in the tryptophan operon using global optimization. Although a number of models for this biochemical network are proposed, in many cases only qualitative agreement between the model output and experimental data was demonstrated, since very little information is currently available to guide the selection of parameter values for the models. This paper presents a model validating method using both multiple experimental data and global ...
KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized al... more KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized alien translocations and promoting exchanges between crop and wild genomes. Resistance to mustard aphid (Lipaphis erysimi) infestation was significantly improved in Brassica juncea through B. juncea-B. fruticulosa introgression. However, linkage drag caused by introgressed chromatin fragments has so far prevented the deployment of this resistance source in commercial cultivars. We investigated the patterns of donor chromatin segment substitutions in the introgression lines (ILs) through genomic in situ hybridization (GISH) coupled with B. juncea chromosome-specific oligonucleotide probes. These allowed identification of large chromosome translocations from B. fruticulosa in the terminal regions of chromosomes A05, B02, B03 and B04 in three founder ILs (AD-64, 101 and 104). Only AD-101 carried an additional translocation at the sub-terminal to intercalary position in both homologues of chromosome A01. We validated these translocations with a reciprocal blast hit analysis using shotgun sequencing of three ILs and species-specific contigs/scaffolds (kb sized) from a de novo assembly of B. fruticulosa. Alien segment substitution on chromosome A05 could not be validated. Current studies also endeavoured to break linkage drag by exposing seeds to a heavy dose (200kR) of gamma radiation. Reduction in the size of introgressed chromatin fragments was observed in many M3 plants. There was a complete loss of the alien chromosome fragment in one instance. A few M3 plants with novel patterns of chromosome segment substitutions displayed improved agronomic performance coupled with resistance to mustard aphid. SNPs in such genomic spaces should aid the development of markers to track introgressed DNA and allow application in plant breeding.
Table S7. RepeatExplorer characterization of selected repeat clusters of four Avena species. Char... more Table S7. RepeatExplorer characterization of selected repeat clusters of four Avena species. Characterization of repetitive fragments used as FISH probes from k-mer or RepeatExplorer analyses of Avena species. Genome proportion, domain hits, contig length and FISH figure references are listed. (DOCX 24 kb)
Figure S12. Analysis of neighboring RepeatExplorer clusters. The interactive graphs showing selec... more Figure S12. Analysis of neighboring RepeatExplorer clusters. The interactive graphs showing selected clusters harboring FISH probes used in the present study (red circles) with 1st order neighbors with at least one connection (green circles). Connection between two neighboring clusters shown by grey and black lines along with similar read number. a 312CL82. b 312CL83. c 312CL119. d 312CL125. e 312CL133. f 312CL151. g 312CL153. h 289CL18. i 289CL19. j 289CL93. k 289CL105. l 289CL126. m 289CL145. n 289CL159. o 289CL166. p 299CL31. q 299CL52. r 315CL87. s 315CL116. t 315CL125. Clusters with at least one neighbor shown in circle. Remaining clusters 289CL148, 289CL187, 299CL118, 299CL125, 299CL126, 312CL175, 315CL155, 315CL171 and 315CL176 without any one neighbor. Black letters denote tandem repeats (b, c, f-g, j-k, m-o, s-t) and brown-red letters denote linear cluster graphs of non-tandem repeats (a, d-e, h-i, l, p-r). (JPG 457 kb)
Background: We consider the problem of identifying the dynamic interactions in biochemical networ... more Background: We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS) estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS). The Total Least Squares (TLS) technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with timeseries measurements of concentrations and expression profiles in gene networks. Results: The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and mdm2 messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL)-6 and (IL)-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL)-6 and (IL)-12b by ATF3. Conclusion: The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable more accurate and reliable identification and modelling of biochemical networks.
ABSTRACT The self-incompatibility type is of key importance to understanding pollination in orcha... more ABSTRACT The self-incompatibility type is of key importance to understanding pollination in orchards, because most olive cultivars are partially self-incompatible and thus require pollinizers to ensure fruit set. The gametophytic model has been advocated to function in the olive, but no allele pair has been attributed to any variety. The SI model failed in most combinations to explain fruit set. Olive growers must screen experimentally and empirically to look for inter-compatible pair-wise combinations of varieties for optimum pollination. The sporophytic model, with given dominance relationships for six S-alleles matches 98 % of the experimental data of the two sets investigated. We propose a method to analyze data from controlled crosses between olive cultivars applied to two experiments for varieties crossed in a diallel design. Furthermore, the dominance between the S-allele pair allows rational prediction of olive variety self-incompatibility levels. The S-allele pairs were unraveled for more than 60 cultivars. To go further, crosses between reference varieties— those in which the S-allele pair was unraveled—and varieties under experimentation (VarE) with an unknown S-allele pair will enable an increase in knowledge and the choice of the best pollinizers in silico. Nevertheless, we pose outstanding questions in orchards where open-pollination efficiency with varieties harboring the R2R3, R1R3, R1R5, or R3R5 pairs. These S-allele pairs require pollen grains without R2 or R3, R1 or R3, and R3 or R5 determinants. Such pollinizer varieties are not abundant in France and Italy, and this questions whether their spread is sufficient for optimal pollination of main varieties.
Abstract In a search for repetitive DNA sequences in the sugar beet genome, two sequences with re... more Abstract In a search for repetitive DNA sequences in the sugar beet genome, two sequences with repeat unit lengths of 143 and 434 bp were isolated and characterized. The pSV family showed an unusual conservation of restriction sites reflecting homogenization of the analyzed repeats. Members of the family are organized as tandem repeats as revealed by PCR and sequencing of dimeric units. The pSV satellite occurs in large intercalary arrays which are present on all chromosome arms of sugar beet. The pSV sequence family is ...
Stable and robust oscillations in the concentration of adenosine 39, 59-cyclic monophosphate (cAM... more Stable and robust oscillations in the concentration of adenosine 39, 59-cyclic monophosphate (cAMP) are observed during the aggregation phase of starvation-induced development in Dictyostelium discoideum. In this paper we use mathematical modelling together with ideas from robust control theory to identify two factors which appear to make crucial contributions to ensuring the robustness of these oscillations. Firstly, we show that stochastic fluctuations in the molecular interactions play an important role in preserving stable oscillations in the face of variations in the kinetics of the intracellular network. Secondly, we show that synchronisation of the aggregating cells through the diffusion of extracellular cAMP is a key factor in ensuring robustness of the oscillatory waves of cAMP observed in Dictyostelium cell cultures to cell-to-cell variations. A striking and quite general implication of the results is that the robustness analysis of models of oscillating biomolecular networks (circadian clocks, Ca 2þ oscillations, etc.) can only be done reliably by using stochastic simulations, even in the case where molecular concentrations are very high.
We examined the diversity, evolution, and genomic organization of retroelements in a wide range o... more We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.
Molecular cytogenetic methods have been used to study the controversial phylogenetic relationship... more Molecular cytogenetic methods have been used to study the controversial phylogenetic relationships between the species Dasypyrum villosum (L.) Candargy (2n=2x=14) and D. breviaristatum (Lindb. f.) Frederiksen (2n=4x=28). Using total genomic DNA from the two species as probes for in situ hybridization to chromosomes, we found that the pericentromeric regions of the chromosome arms of both species are similar, while distal regions show substantial differences. Two dispersed repetitive DNA sequences were isolated: pDbKB45 is distributed along the chromosomes but amplified in the subtelomeric regions of D. breviaristatum chromosomes, while pDbKB49, in both species, is less amplified in terminal regions. Size-separated restriction enzyme digests of DNA showed many repetitive fragments, but few in common between the two species. After probing Southern transfers with D. breviaristatum genomic DNA, all lanes showed similar hybridization patterns although one extra small band was evident in the D. breviaristatum lanes. In contrast, probing with D. villosum DNA showed very substantial differences between the two species. Genomic in situ hybridization to meiotic metaphases from an interspecific hybrid showed seven bivalents of D. breviaristatum origin and seven univalents from D. villosum. We also analysed the physical organization of 5S rDNA, 18S-25S rDNA and a tandemly repeated sequence from rye. Our data support an autotetraploid origin for D. breviaristatum, but its genome and that of D. villosum show extensive differences, so the tetraploid is unlikely to be directly derived from D. villosum.
In most molecular level simulations, spatial heterogeneity is neglected by the well-mixed conditi... more In most molecular level simulations, spatial heterogeneity is neglected by the well-mixed condition assumption. However, the signals of biomolecular networks are affected from both time and space, which are responsible for diverse physiological responses. To account the spatial heterogeneity in the kinetic model, we consider multiple subvolumes of a reaction, introduce parameters representing transfer of ligands between the volumes, and reduce this to an error-term representing the difference between the well-mixed condition and the ...
Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J. (2010) Efficient stochastic simulation alg... more Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J. (2010) Efficient stochastic simulation algorithm including intrinsic noise and extrinsic noise from spatial molecular heterogeneity. In: 11th ICSB-2010 Conference, 10-15 Oct 2010, Edinburgh, UK. ... Full text not currently available from Enlighten. ... Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J.
Contemporary Issues in Genetics and Evolution, 1997
Retrotransposons make up a major fraction-sometimes more than 40%-of all plant genomes investigat... more Retrotransposons make up a major fraction-sometimes more than 40%-of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of the Tyl-copia group elements from several species, ranging in genome size from some 100 Mbp to 23 000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and within interphase nuclei by DNA:DNA in situ hybridization. With some exceptions, the reverse transcriptase domains were distributed over the length of the chromosomes. Exclusion from rDNA sites and some centromeres (e.g., slash pine, 23 000 Mbp, or barley, 5500 Mbp) is frequent, whereas many species exclude retrotransposons from other sites of heterochromatin (e.g., intercalary and centromeric sites in broad bean). In contrast, in the plant Arabidopsis thaliana, widely used for plant molecular genetic studies because of its small genome (c. 100 Mbp), the Tyl-copia group reverse transcriptase gene domains are concentrated in the centromeric regions, collocalizing with the 180 bp satellite sequence pAL1. Unlike the pAL1 sequence, however, the Tylcopia signal is also detectable as weaker, diffuse hybridization along the lengths of the chromosomes. Possible mechanisms for evolution of the contrasting distributions are discussed. Understanding the physical distribution of retrotransposons and comparisons of the distribution between species is critical to understanding their evolution and the significance for generation of the new patterns of variability and in speciation.
Figure S4. Fluorescent in situ hybridization (FISH) karyotyping of Avena sativa. Probes are AF226... more Figure S4. Fluorescent in situ hybridization (FISH) karyotyping of Avena sativa. Probes are AF226603_45bp (direct TET, red) for the C genome, pAs120a (biotin, Alexa 594, blue) for the A genome, and Ast-R171 (digoxigenin, FITC, green) for the D genome. On the right the DAPI image of chromosomes is shown in white, in the middle the same metaphase shows hybridization signal from all three probes except in (d) where only AF226603_45bp in yellow and pAs120 in blue are visible. Probes were amplified from different diploid species. a A. brevis. b A. atlantica. c A. strigosa. d A. wiestii. e A. longiglumis. f A. hirtula. In the karyotypes (on the left), chromosomes are arranged in rows corresponding to genome origin: 1–14 C-genome, 15–28 A-genome, and 29–42 D-genome. White stars, arrows, and arrowheads denoted C-, A-, and D-chromosome regions, translocated to a different genome: there are C translocations on 12 D-chromosomes (29–40); A translocations on four C-chromosomes (5/6 & 11/12); D t...
Figure S3. Localization of selected C-genome specific repetitive sequences on Avena sativa metaph... more Figure S3. Localization of selected C-genome specific repetitive sequences on Avena sativa metaphase chromosomes by multicolour FISH. Probe signals were captured individually with a black and white CCD camera and then pseudo-coloured to create overlaid images. For detailed description of signal distribution see Additional file 21: Table S9. a AF226603_45bp (hybridization sites displayed in red), Ab-R18 amplified from A. atlantica (green), and pAs120a from A. atlantica (blue). Note that overlapping signals of the red and green probe give yellow signals. b Ab-R19 (red) and Ab-R126 (green), counterstain DAPI (blue) shown on all chromosomes. Note that overlapping signals of the red and green probe appear white, but show several chromosome ends not labelled by either probe appearing blue or show green double dots. c AF226603_45bp (red), Ah-T118 from A. hirtula (green), and pAs120a from A. hirtula (blue). Overlapping signals of the red and green probe appear yellow and show non-uniform la...
This paper is concerned with validating a mathematical model of regulation in the tryptophan oper... more This paper is concerned with validating a mathematical model of regulation in the tryptophan operon using global optimization. Although a number of models for this biochemical network are proposed, in many cases only qualitative agreement between the model output and experimental data was demonstrated, since very little information is currently available to guide the selection of parameter values for the models. This paper presents a model validating method using both multiple experimental data and global ...
KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized al... more KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized alien translocations and promoting exchanges between crop and wild genomes. Resistance to mustard aphid (Lipaphis erysimi) infestation was significantly improved in Brassica juncea through B. juncea-B. fruticulosa introgression. However, linkage drag caused by introgressed chromatin fragments has so far prevented the deployment of this resistance source in commercial cultivars. We investigated the patterns of donor chromatin segment substitutions in the introgression lines (ILs) through genomic in situ hybridization (GISH) coupled with B. juncea chromosome-specific oligonucleotide probes. These allowed identification of large chromosome translocations from B. fruticulosa in the terminal regions of chromosomes A05, B02, B03 and B04 in three founder ILs (AD-64, 101 and 104). Only AD-101 carried an additional translocation at the sub-terminal to intercalary position in both homologues of chromosome A01. We validated these translocations with a reciprocal blast hit analysis using shotgun sequencing of three ILs and species-specific contigs/scaffolds (kb sized) from a de novo assembly of B. fruticulosa. Alien segment substitution on chromosome A05 could not be validated. Current studies also endeavoured to break linkage drag by exposing seeds to a heavy dose (200kR) of gamma radiation. Reduction in the size of introgressed chromatin fragments was observed in many M3 plants. There was a complete loss of the alien chromosome fragment in one instance. A few M3 plants with novel patterns of chromosome segment substitutions displayed improved agronomic performance coupled with resistance to mustard aphid. SNPs in such genomic spaces should aid the development of markers to track introgressed DNA and allow application in plant breeding.
Table S7. RepeatExplorer characterization of selected repeat clusters of four Avena species. Char... more Table S7. RepeatExplorer characterization of selected repeat clusters of four Avena species. Characterization of repetitive fragments used as FISH probes from k-mer or RepeatExplorer analyses of Avena species. Genome proportion, domain hits, contig length and FISH figure references are listed. (DOCX 24 kb)
Figure S12. Analysis of neighboring RepeatExplorer clusters. The interactive graphs showing selec... more Figure S12. Analysis of neighboring RepeatExplorer clusters. The interactive graphs showing selected clusters harboring FISH probes used in the present study (red circles) with 1st order neighbors with at least one connection (green circles). Connection between two neighboring clusters shown by grey and black lines along with similar read number. a 312CL82. b 312CL83. c 312CL119. d 312CL125. e 312CL133. f 312CL151. g 312CL153. h 289CL18. i 289CL19. j 289CL93. k 289CL105. l 289CL126. m 289CL145. n 289CL159. o 289CL166. p 299CL31. q 299CL52. r 315CL87. s 315CL116. t 315CL125. Clusters with at least one neighbor shown in circle. Remaining clusters 289CL148, 289CL187, 299CL118, 299CL125, 299CL126, 312CL175, 315CL155, 315CL171 and 315CL176 without any one neighbor. Black letters denote tandem repeats (b, c, f-g, j-k, m-o, s-t) and brown-red letters denote linear cluster graphs of non-tandem repeats (a, d-e, h-i, l, p-r). (JPG 457 kb)
Background: We consider the problem of identifying the dynamic interactions in biochemical networ... more Background: We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS) estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS). The Total Least Squares (TLS) technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with timeseries measurements of concentrations and expression profiles in gene networks. Results: The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and mdm2 messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL)-6 and (IL)-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL)-6 and (IL)-12b by ATF3. Conclusion: The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable more accurate and reliable identification and modelling of biochemical networks.
ABSTRACT The self-incompatibility type is of key importance to understanding pollination in orcha... more ABSTRACT The self-incompatibility type is of key importance to understanding pollination in orchards, because most olive cultivars are partially self-incompatible and thus require pollinizers to ensure fruit set. The gametophytic model has been advocated to function in the olive, but no allele pair has been attributed to any variety. The SI model failed in most combinations to explain fruit set. Olive growers must screen experimentally and empirically to look for inter-compatible pair-wise combinations of varieties for optimum pollination. The sporophytic model, with given dominance relationships for six S-alleles matches 98 % of the experimental data of the two sets investigated. We propose a method to analyze data from controlled crosses between olive cultivars applied to two experiments for varieties crossed in a diallel design. Furthermore, the dominance between the S-allele pair allows rational prediction of olive variety self-incompatibility levels. The S-allele pairs were unraveled for more than 60 cultivars. To go further, crosses between reference varieties— those in which the S-allele pair was unraveled—and varieties under experimentation (VarE) with an unknown S-allele pair will enable an increase in knowledge and the choice of the best pollinizers in silico. Nevertheless, we pose outstanding questions in orchards where open-pollination efficiency with varieties harboring the R2R3, R1R3, R1R5, or R3R5 pairs. These S-allele pairs require pollen grains without R2 or R3, R1 or R3, and R3 or R5 determinants. Such pollinizer varieties are not abundant in France and Italy, and this questions whether their spread is sufficient for optimal pollination of main varieties.
Abstract In a search for repetitive DNA sequences in the sugar beet genome, two sequences with re... more Abstract In a search for repetitive DNA sequences in the sugar beet genome, two sequences with repeat unit lengths of 143 and 434 bp were isolated and characterized. The pSV family showed an unusual conservation of restriction sites reflecting homogenization of the analyzed repeats. Members of the family are organized as tandem repeats as revealed by PCR and sequencing of dimeric units. The pSV satellite occurs in large intercalary arrays which are present on all chromosome arms of sugar beet. The pSV sequence family is ...
Stable and robust oscillations in the concentration of adenosine 39, 59-cyclic monophosphate (cAM... more Stable and robust oscillations in the concentration of adenosine 39, 59-cyclic monophosphate (cAMP) are observed during the aggregation phase of starvation-induced development in Dictyostelium discoideum. In this paper we use mathematical modelling together with ideas from robust control theory to identify two factors which appear to make crucial contributions to ensuring the robustness of these oscillations. Firstly, we show that stochastic fluctuations in the molecular interactions play an important role in preserving stable oscillations in the face of variations in the kinetics of the intracellular network. Secondly, we show that synchronisation of the aggregating cells through the diffusion of extracellular cAMP is a key factor in ensuring robustness of the oscillatory waves of cAMP observed in Dictyostelium cell cultures to cell-to-cell variations. A striking and quite general implication of the results is that the robustness analysis of models of oscillating biomolecular networks (circadian clocks, Ca 2þ oscillations, etc.) can only be done reliably by using stochastic simulations, even in the case where molecular concentrations are very high.
We examined the diversity, evolution, and genomic organization of retroelements in a wide range o... more We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.
Molecular cytogenetic methods have been used to study the controversial phylogenetic relationship... more Molecular cytogenetic methods have been used to study the controversial phylogenetic relationships between the species Dasypyrum villosum (L.) Candargy (2n=2x=14) and D. breviaristatum (Lindb. f.) Frederiksen (2n=4x=28). Using total genomic DNA from the two species as probes for in situ hybridization to chromosomes, we found that the pericentromeric regions of the chromosome arms of both species are similar, while distal regions show substantial differences. Two dispersed repetitive DNA sequences were isolated: pDbKB45 is distributed along the chromosomes but amplified in the subtelomeric regions of D. breviaristatum chromosomes, while pDbKB49, in both species, is less amplified in terminal regions. Size-separated restriction enzyme digests of DNA showed many repetitive fragments, but few in common between the two species. After probing Southern transfers with D. breviaristatum genomic DNA, all lanes showed similar hybridization patterns although one extra small band was evident in the D. breviaristatum lanes. In contrast, probing with D. villosum DNA showed very substantial differences between the two species. Genomic in situ hybridization to meiotic metaphases from an interspecific hybrid showed seven bivalents of D. breviaristatum origin and seven univalents from D. villosum. We also analysed the physical organization of 5S rDNA, 18S-25S rDNA and a tandemly repeated sequence from rye. Our data support an autotetraploid origin for D. breviaristatum, but its genome and that of D. villosum show extensive differences, so the tetraploid is unlikely to be directly derived from D. villosum.
In most molecular level simulations, spatial heterogeneity is neglected by the well-mixed conditi... more In most molecular level simulations, spatial heterogeneity is neglected by the well-mixed condition assumption. However, the signals of biomolecular networks are affected from both time and space, which are responsible for diverse physiological responses. To account the spatial heterogeneity in the kinetic model, we consider multiple subvolumes of a reaction, introduce parameters representing transfer of ligands between the volumes, and reduce this to an error-term representing the difference between the well-mixed condition and the ...
Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J. (2010) Efficient stochastic simulation alg... more Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J. (2010) Efficient stochastic simulation algorithm including intrinsic noise and extrinsic noise from spatial molecular heterogeneity. In: 11th ICSB-2010 Conference, 10-15 Oct 2010, Edinburgh, UK. ... Full text not currently available from Enlighten. ... Zhao, Y.-B., Mao, X., Heslop-Harrison, P., and Kim, J.
Contemporary Issues in Genetics and Evolution, 1997
Retrotransposons make up a major fraction-sometimes more than 40%-of all plant genomes investigat... more Retrotransposons make up a major fraction-sometimes more than 40%-of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of the Tyl-copia group elements from several species, ranging in genome size from some 100 Mbp to 23 000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and within interphase nuclei by DNA:DNA in situ hybridization. With some exceptions, the reverse transcriptase domains were distributed over the length of the chromosomes. Exclusion from rDNA sites and some centromeres (e.g., slash pine, 23 000 Mbp, or barley, 5500 Mbp) is frequent, whereas many species exclude retrotransposons from other sites of heterochromatin (e.g., intercalary and centromeric sites in broad bean). In contrast, in the plant Arabidopsis thaliana, widely used for plant molecular genetic studies because of its small genome (c. 100 Mbp), the Tyl-copia group reverse transcriptase gene domains are concentrated in the centromeric regions, collocalizing with the 180 bp satellite sequence pAL1. Unlike the pAL1 sequence, however, the Tylcopia signal is also detectable as weaker, diffuse hybridization along the lengths of the chromosomes. Possible mechanisms for evolution of the contrasting distributions are discussed. Understanding the physical distribution of retrotransposons and comparisons of the distribution between species is critical to understanding their evolution and the significance for generation of the new patterns of variability and in speciation.
Figure S4. Fluorescent in situ hybridization (FISH) karyotyping of Avena sativa. Probes are AF226... more Figure S4. Fluorescent in situ hybridization (FISH) karyotyping of Avena sativa. Probes are AF226603_45bp (direct TET, red) for the C genome, pAs120a (biotin, Alexa 594, blue) for the A genome, and Ast-R171 (digoxigenin, FITC, green) for the D genome. On the right the DAPI image of chromosomes is shown in white, in the middle the same metaphase shows hybridization signal from all three probes except in (d) where only AF226603_45bp in yellow and pAs120 in blue are visible. Probes were amplified from different diploid species. a A. brevis. b A. atlantica. c A. strigosa. d A. wiestii. e A. longiglumis. f A. hirtula. In the karyotypes (on the left), chromosomes are arranged in rows corresponding to genome origin: 1–14 C-genome, 15–28 A-genome, and 29–42 D-genome. White stars, arrows, and arrowheads denoted C-, A-, and D-chromosome regions, translocated to a different genome: there are C translocations on 12 D-chromosomes (29–40); A translocations on four C-chromosomes (5/6 & 11/12); D t...
Figure S3. Localization of selected C-genome specific repetitive sequences on Avena sativa metaph... more Figure S3. Localization of selected C-genome specific repetitive sequences on Avena sativa metaphase chromosomes by multicolour FISH. Probe signals were captured individually with a black and white CCD camera and then pseudo-coloured to create overlaid images. For detailed description of signal distribution see Additional file 21: Table S9. a AF226603_45bp (hybridization sites displayed in red), Ab-R18 amplified from A. atlantica (green), and pAs120a from A. atlantica (blue). Note that overlapping signals of the red and green probe give yellow signals. b Ab-R19 (red) and Ab-R126 (green), counterstain DAPI (blue) shown on all chromosomes. Note that overlapping signals of the red and green probe appear white, but show several chromosome ends not labelled by either probe appearing blue or show green double dots. c AF226603_45bp (red), Ah-T118 from A. hirtula (green), and pAs120a from A. hirtula (blue). Overlapping signals of the red and green probe appear yellow and show non-uniform la...
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Papers by John Heslop-harrison