Repetitive DNA in the catfish genome- rDNA, microsatellites, and Tc1-mariner transposon sequences in Imparfinis

Repetitive sequence organization on chromosomes of a Brazilian catfish species, important for understanding their evolution and biodiversity. Gouveia et al., Journal of Heredity, 2017.

Repetitive sequence organization on chromosomes of a Brazilian catfish species, important for understanding their evolution and biodiversity. Gouveia et al., Journal of Heredity, 2017.

339. Gouveia JG, Wolf IR, Vilas-Boas LA, Heslop-Harrison JS, Schwarzacher T, Dias AL. 2017. Repetitive DNA in the catfish genome: rDNA, microsatellites, and Tc1-mariner transposon sequences in Imparfinis species (Siluriformes, Heptapteridae). Journal of Heredity 108(6): 650-657.

Journal link: https://doi.org/10.1093/jhered/esx065 Author PHHGouveia_CatfishRepeatsAuthorVersion

Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I.  schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I.  schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.

Subject area: Genomics and gene mapping
Key words: genome evolution, karyotype evolution, MITEs, transposable elements

Advertisements
Posted in animals, Collaborators, Publications, Species | Tagged , , , , , , , , , , , , , , | Leave a comment

Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants

337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120(2): 183-194. https://doi.org/10.1093/aob/mcx079  (Free access).

Polyploidy, defined as whole genome duplication, is present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. This Annals of Botany Special Issue on Polyploidy in Ecology and Evolution presents the evolutionary consequences of new, recent, and ancient polyploidy. Alix et al. survey experimental, genomic, ecological and theoretical studies demonstrating that polyploidization often occurs during periods of major evolutionary transitions and adaptive radiation of species. Polyploidy, the cornerstone of bursts of adaptive speciation, brings about genetic novelty. The emergence of new gene functions enables diversification, speciation, and hence plant evolution.

The figure can be downloaded in Powerpoint format here AlixSchwarzacherHeslopHarrisonPlantEvolutionPolyploidyWGDAnnalsBotany format.

Background Polyploidy or whole genome duplication is now recognized as being
present in almost all lineages of higher plants, with multiple rounds of polyploidy
occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridisation events are found in about half of the world’s crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this article, consider genomic aspects of polyploidy.
• Approaches Discovery of the evolutionary consequences of new, evolutionarily
recent, and ancient polyploidy requires a range of approaches. Large scale studies of
both single species, and whole ecosystems, with hundreds to tens of thousands of
individuals, sometimes involving ‘garden’ or transplant experiments are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution, require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.
• Conclusions The success of polyploidy, displacing the diploid ancestors of almost all
plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidisation events. Strikingly, polyploidisation often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting that concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole genome duplication act as a driver of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

Key words: Polyploidy, hybrids, ecology, adaptation, evolution, genomics, chromosomes, speciation, whole genome duplication (WGD), crops, weeds, phylogeny, bryophytes,
angiosperms

Published version: https://doi.org/10.1093/aob/mcx079  (Free access).

And

AlixPolyploidy2017AuthorVersion.

 

Update 16/8/2017 to add author version (although original is free acces) and page reference.

Posted in Brassica, cereals, Publications, wheat | Tagged , , , , , , , , , , , | Leave a comment

Identification and characterization of mobile genetic elements LINEs from Brassica genome

Nouroz F, Noreen S, Khan MF, Ahmed S, Heslop-Harrison JS. 2017. Identification and characterization of mobile genetic elements LINEs from Brassica genomes. Gene in press June 2017.

Abstract
Among transposable elements (TEs), the LTR retrotransposons are abundant followed by nonLTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four nonautonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to ‘R’ and ‘I’ type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were
observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars.

Keywords: Retrotransposons, Brassica, LINEs, Reverse transcriptase, Diversity, Phylogeny.

Posted in Brassica, Publications, Uncategorized | Tagged , , , , , , , , , , , , | Leave a comment

Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants

Fig1PolyploidyAlixEtAl.jpg337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120: 183–194. https://dx.doi.org/10.1093/aob/mcx079 (freely available)

Author version (free to post) to come. Figure 1 showing polyploidy or WGD whole genome duplication events in plant evolution is here AlixSchwarzacherHeslopHarrisonPlantEvolutionPolyploidyWGDAnnalsBotany (Powerpoint format)

  • Background. Polyploidy or whole genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridisation events are found in about half of the world’s crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this article, consider genomic aspects of polyploidy.
  • Discovery of the evolutionary consequences of new, evolutionarily recent, and ancient polyploidy requires a range of approaches. Large scale studies of both single species, and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving ‘garden’ or transplant experiments are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution, require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.
  • Conclusions: The success of polyploidy, driving out the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidisation events. Strikingly, polyploidisation often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting that concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole genome duplication act as a driver of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

 

Keywords: Polyploidy, hybrids, ecology, adaptation, evolution, genomics, chromosomes, speciation, whole genome duplication (WGD), crops, weeds, phylogeny, bryophytes, angiosperms

337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120: 183–194. https://dx.doi.org/10.1093/aob/mcx079

Posted in Uncategorized | Tagged , , , , , , , , , , , | Leave a comment

New Project on Molecular Cytogenetics and Genomics of Ensete banana

Stachy enset (Ensete ventricosum) corms held by children in a smallholding in Ethiopia, where enset starch is an important staple and food security crop.

Starchy enset (Ensete ventricosum) corms held by children in a smallholding in Ethiopia, where enset is an important staple and food security crop.

We have a research project starting in 2017 on Ethiopian banana, Ensete ventricosum, for 18 months, in collaboration with Royal Botanic Gardens, Kew (Dr Paul Wilkin) and University of Addis Ababa (Professor Sebsebe Demissew). There is a post-doctoral position working with the project (closed 7 August 2017).

The project “Modelling and genomics resources to enhance exploitation of the sustainable and diverse Ethiopian starch crop Enset” is funded by the Global Challenges Research Fund under a Foundation Award for Global Agricultural and Food Systems Research from the Biotechnology and Biological Sciences Research Council (BBSRC).

Our exciting interdisciplinary project seeks to provide the foundation knowledge to help enable the exploitation of the sustainable and diverse Ethiopian starch crop Enset (Musaceae) to support livelihoods in Africa. To this end, we will integrate genomic sequence, molecular diversity, pathology, tissue culture and cytogenetic data, with field and farmer interview data from Ethiopia.

The researcher on the project will be responsible for carrying out and publishing the genomic and laboratory components of the project. You will lead, conduct, and manage a significant laboratory and informatics project in Leicester, UK, integrating your research with field work, working with the lead Ethiopian partner (Addis Ababa University) and modelling at the Royal Botanic Gardens, Kew, under the guidance of the project team.

The work requires experience in plant molecular biology, markers, cytogenetics and genomics or bioinformatics. Ideally this would involve species (crops) with little background data.

Enquiries about the research are welcome and should be made to Prof Pat Heslop-Harrison on phh4@le.ac.uk or 0794 603 4502 or 0116 252 5079 and Dr Trude Schwarzacher on ts32@le.ac.uk or 07964295126. (We anticipate that assessments will take place on 18 or 21 August 2017.)

More information about our Ensete project is given at https://molcyt.org/2017/01/17/banana-ensete-and-boesenbergia-genomics-talk-by-schwarzacher-heslop-harrison-harikrishna/, including a lecture which should have been given to an Ensete audience in Addis Ababa, Ethiopia on YouTube, and slides from a lecture at the Plant and Animal Genome PAG conference, San Diego, January 2017 (slides also on Slideshare). Our lab publication page has other relevant information.

 

MAJOR REVISION to the above information and page 9 August 2017 after the application deadline for the research position.

 

 

Posted in Collaborators, Farming, jobs, Musa, People, Research, Species | Tagged , , , , , , , , , , , , , , , , , , , , , , , | Leave a comment

The landscape and structural diversity of LTR Retrotransposons in the Musa genome

Nouroz et al. LTR retrotransposons in Musa. Mol Gen Genomics 2017

334. Nouroz F, Noreen S, Ahmad H, Heslop Harrison JS(P). 2017. The landscape and structural diversity of LTR Retrotransposons in the Musa genome. Molecular Genetics and Genomics 292: 1051-1067. http://dx.doi.org/10.1007/s00438-017-1333-1 Publisher site (££$$€€ needs subscription)

Author version of manuscript: Nouroz_MGG2017_MusaLTRretrotransposons_AuthorVer

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae and Copia lineages. Most of the Musa related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation and evolutionary dynamics in the Musa genome.

Keywords: Musa, retrotransposons, Copia, Gypsy, Biodiversity, phylogeny, genomics, evolution.

Posted in Musa, Publications, Species | Tagged , , , , , , , , , | Leave a comment

Molecular Diversity in some Ghanaian cowpea (Vigna unguiculata) accessions

315. Otwe EP, Agyirifo DS, Galyuon IK, Heslop-Harrison JS. 2017. Molecular Diversity in some Ghanaian Cowpea [Vigna unguiculata L.(Walp)] Accessions. Tropical Plant Biology.:1-11. DOI 10.1007/s12042-017-9184-9
BibT

Cowpea [Vigna unguiculata L. (Walp)] is grown mainly for its protein-rich grains and is consumed in various forms in sub-Saharan Africa. Average grain yield in farmers’ fields is generally low due to a number of biotic and abiotic stresses. One hundred and six cowpea accessions from Ghana, which had previously been evaluated for seedling drought tolerance, were used for this study. This paper attempts to use three multi-locus PCR-based molecular markers; simple sequence repeats (SSR), inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphisms (REMAP), to analyse genetic diversity in the cowpea accessions. Analysis of the polymorphic bands data indicated that 101 alleles were amplified among 121 cowpea genotypes (83.4%) from 16 SSR primer pairs out of a total of 30 SSR primer pairs. Likewisely, a total of 66 (54.5%) polymorphic bands were obtained from IRAP and a total of 114 (94.2%) highly polymorphic bands obtained from REMAP analysis. The outcome indicated the highly polymorphic nature of the DNA markers, as small groups of these molecular markers were found to be able to identify each of the accessions used. Microsatellite markers (SSRs) and retrotransposon-based markers, like IRAP and REMAP, were found to be highly polymorphic and informative, suggesting that genomic fingerprinting has a major role in characterizing populations

Posted in Uncategorized | Leave a comment