Banana research at the botanic garden

Banana fruit bunch with male flower

Banana fruit bunch with male flower

324. Heslop-Harrison, P. 2015. Banana research at the botanic garden. University of Leicester Botanic Garden Newsletter 12: 4. November 2015.

Dessert bananas and the cooking bananas or plantains are among the oldest crops in the world. Most crops were domesticated through a long pathway of selection and crossing but, for banana, virtually all the two thousand varieties which are grown throughout the tropics were collected as spontaneous mutants in the wild with the extraordinary property of having large fleshy fruit without any seeds. Most varieties of banana are also unusual in having three sets of chromosomes, a condition known as triploid.

The wild progenitors of the domesticated banana are from south-east Asia and are currently known as Musa acuminata (with a genome designated as ‘A’, green on the map below) and Musa balbisiana (with a ‘B’ genome, orange on the map below). About 15% of the world’s banana production is for the export trade, and is based on a single variety, ‘Cavendish’. This sweet banana has the genome constitution AAA. Banana varieties that are hybrids with AAB and ABB genome constitutions are a staple food for a billion people in Asia and Africa, and in Leicester we are fortunate that many of these plantains and cooking bananas (eaten fried or steamed and mashed as a vegetable) are easily available in the market and speciality shops.

In many parts of Asia, banana leaves are also used as disposable plates or as wrappers for steaming rice or banana fruit. Interestingly, there is now the possibility that these two currently recognized A and B species will be merged into one; this would probably mean resurrecting one of the original names given by Linneaus, Musa paradisiaca L. or Musa sapientum L.

Traditionally, bananas are propagated by side suckers to the main stem but, in commercial plantations, most plants are now multiplied through tissue culture to ensure disease-free planting material. In our research group, we study the diversity and evolution of bananas at the DNA level, and are looking for new diversity to improve current varieties. The amount of DNA in plant genomes varies widely, from less than 100 Mbp in some carnivorous plants such as Genlisea, to more than 17,000 Mbp in wheat and pines. Bananas are at the lower end of the range, with about 550 Mbp. We were involved in the international consortium that sequenced all the DNA in banana in 2012, and thus we have a reference for all the genes and regulatory sequences present in the species.

This is vital if breeding programmes are to produce new disease-resistant varieties. Disease is a major problem in banana production in the topics: bananas suffer from fungi, bacteria, viruses, insects and nematodes. About a third of the cost of growing the bananas is spent on crop protection chemicals, and all fruit bunches are covered with blue bags to deter insects from damaging the fruit and allowing entry of secondary fungal. Eradication of disease in some areas costs millions of pounds and requires destruction of millions of plants. Very careful agronomy can control diseases, such as burning plants at the first sign of infection, or dipping machetes in bleach between harvesting each plant, but such measures required huge amounts of training and labour. Some diseases cannot be controlled with agronomy or chemicals, and means banana production is lost to an area. Our current work is looking at the diversity present in the whole banana genome at various positions related to diseases, we are also looking how the variation can be exploited in generating new varieties of banana which are disease resistant.

324. Heslop-Harrison, P. 2015. Banana research at the botanic garden. University of Leicester Botanic Garden Newsletter 12: 4. November 2015.


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Repetitive DNA in eukaryotic genomes

Biscotti et al. 2015. Repetitive DNA in the eukaryotic genome. Chromosome Research

Biscotti et al. 2015. Repetitive DNA in the eukaryotic genome. Chromosome Research

322. Biscotti MA, Olmo E, Heslop-Harrison JS. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23(3): 415-420. DOI: 10.1007/s10577-015-9499-z

Biscotti Repetitive DNA Author Version

Link to Repetitive DNA summary Diagram DNA

Repetitive DNA — sequence motifs repeated hundreds or thousands of times in the genome— makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component.

repetitive DNA, tandem repeats, genomics, junk DNA, transposons, satellite DNA, retrotransposons, review

Biscotti MA, Olmo E, Heslop-Harrison JS. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23(3): 415-420. DOI: 10.1007/s10577-015-9499-z

Biscotti Repetitive DNA Author Version

Link to Repetitive DNA summary Diagram DNA

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Innovative science and blue-sky research

Seagull in blue sky - what research needs

Seagull in blue sky – what research needs

321. Braben DW, Heslop-Harrison JS and 48 others. 2015. Letter: Innovative science, Blue Sky research, scientific enterprise and prosperity. The Times (London) 23 September 2015. p. 28.  ( ££)

The Times (London) September 23, 2015 Wednesday Edition 1;
Letter on Innovative science

Sir, “Blue sky” research is vital to scientific enterprise and prosperity, yet it is increasingly hard to find funding for truly innovative projects. First, universities must approve all proposals that are submitted. Funding agencies then subject all proposals they receive to peer review, a process by which a few researchers, usually acting anonymously, assess the proposal’s chances of achieving its goals, whether it offers the best value for money, is relevant to a priority and has an impact on a socioeconomic problem. Only about 25 per cent of proposals win funding. These processes force researchers to exploit existing knowledge, discourage open ended studies, and are hugely time consuming. They are also new: before 1970, few researchers wrote proposals. Now they are effectively mandatory.

Globally, the 20th century was dominated by some 500 Nobel prizewinning academics who explored new concepts, leading to such discoveries as nuclear power, penicillin, lasers, magnetic resonance imaging and monoclonal antibodies.

We must find ways of giving unconstrained support to the tiny number of scientists with radical agendas. BP’s Venture Research initiative for supporting such people ran from 1980 to 1993 and created at least 14 major discoveries from the 37 groups supported. Almost all had been rejected by peer review. Its cost, including BP and university overheads, was about £20 million over 13 years. Identifying people to lead such initiatives will be difficult – but it must be done.

Donald W Braben, UCL; Peter Edwards FRS, University of Oxford; Dame Anne Glover, University of Aberdeen; John Hall, Nobel Laureate, University of Colorado; Dudley Herschbach, Nobel Laureate, Harvard University; Sir Harry Kroto FRS, Nobel Laureate, Florida State University; John Mattick, Garvan Institute of Medical Research, Sydney; Sir Richard J Roberts FRS, Nobel Laureate, New England Biolabs; Ken Seddon, Queen’s University Belfast; Pat Heslop-Harrison, University or Leicester; Plus 40 other senior scientists ££

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Chromosomal distribution and evolution of retrotransposons in diploid and polyploid Brachiaria forage grasses

Brachiaria Retrotransposon Family Distribution: Santos et al. Chromosome Research 2015

319. Santos FC, Guyot R, Valle CB do, Chiari L, Techio VH, Heslop-Harrison P, Vanzela ALL. 2015. Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses. Chromosome Research 23(3): 571-582. DOI: 10.1007/s10577-015-9492-6 Text Brachiaria_Fabiola_Santos_etal AuthorVersion.

Abstract: Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x  = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat exhibited dispersed signals, in addition to those proximal signals. These results show that the proximal region of Brachiaria chromosomes is a hotspot for retrotransposon insertion, particularly for the gypsy family. The combination of high-throughput sequencing and a chromosome-centric cytogenetic approach allows the abundance, organization and nature of transposable elements to be characterized in unprecedented detail. By their amplification and dispersal, retrotransposons can affect gene expression; they can lead to rapid diversification of chromosomes between species and, hence, are useful for studies of genome evolution and speciation in the Brachiaria genus. Centromeric regions can be identified and mapped, and retrotransposon markers can also assisting breeders in the developing and exploiting interspecific hybrids.


centromeres retrotransposons FISH in situ hybridization metaviridae grasses genomics genome organization transposons transposable elements genetics repetitive DNA chromosomes

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319. Santos FC, Guyot R, Valle CB do, Chiari L, Techio VH, Heslop-Harrison P, Vanzela ALL. 2015. Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses. Chromosome Research 23(3): 571-582. DOI: 10.1007/s10577-015-9492-6 Text Brachiaria_Fabiola_Santos_etal AuthorVersion.

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dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid

RNA silencing and flower shape in DendrobiumFlower

RNA silencing and flower shape in Dendrobium orchids

TS. Lau S-E, Schwarzacher T, Othman RY, Harikrishna JA. 2015. dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid. BMC Plant Biology 15, no. 1: 194. DOI 10.1186/s12870-015-0577-3 Local copy Lau et al Dendrobium dsRNA silencing BMCPlant Biology 2015

Background: The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape.

Results: Flower bud development in the Dendrobium hybrid was characterised into seven stages and the time of meiosis was determined as between stages 3 to 5 when the bud is approximately half of the mature size. Scanning electron microscopy characterisation of adaxial epidermal cells of the flower perianth, showed that the petals and sepals each are divided into two distinct domains based on cell shape and size, while the labellum comprises seven domains. Thirty-two partial cDNA fragments representing R2R3-MYB gene sequences were isolated from D. hybrida. Phylogenetic analysis revealed that nine of the translated sequences were clustered with MYB sequences that are known to be involved in cell shape development and from these, DhMYB1 was selected for full length cDNA cloning and functional study. Direct application of a 430 bp dsRNA from the 3’ region of DhMYB1 to emerging orchid flower buds reduced expression of DhMYB1 RNA compared with untreated control. Scanning electron microscopy of adaxial epidermal cells within domain one of the labellum of flowers treated with DhMYB1 dsRNA showed flattened epidermal cells whilst those of control flowers were conical.

Conclusions: DhMYB1 is expressed throughout flower bud development and is involved in the development of the conical cell shape of the epidermal cells of the Dendrobium hybrida flower labellum. The direct application of dsRNA changed the phenotype of floral cells, thus, this technique may have application in floriculture biotechnology.

Keywords: Cell morphogenesis, RNA interference, RNA silencing, Biotechnology, Gene silencing, Epidermal cell

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Molecular characterization and diversity of a novel nonautonomous Mutator-like transposon family in Brassica

Brassica Mutatot-like MULE transposons. Nouroz et al. 2015

Brassica Mutatot-like MULE transposons. Nouroz et al. 2015

320. Nouroz F, Noreen S, Heslop-Harrison JS. 2015. Molecular characterization and diversity of a novel nonautonomous Mutator-like transposon family in Brassica. Pakistani Journal of Botany 47(4): 1367-1375. Publisher abstract Publisher free full text. Local copy BrassicaMutator_Nouroz_PakistaniJBot2015

Transposable elements (TEs) are capable of mobilizing from one genomic location to other, with changes in their copy numbers. Mutator-like elements (MULEs) are DNA transposons characterized by 9 bp target site duplications (TSDs), with high variability in sequence and length, and include non-conserved terminal inverted repeats (TIRs). We identified and characterized a family of Mutator-like elements designated as Shahroz. The structural and molecular analyses revealed that family had a small number of mostly defective non-autonomous MULEs and has shown limited activity in the evolutionary history of the Brassica A-genome. The Shahroz elements range in size from 2734 to 3160 bp including 76 bp imperfect TIRs and 9 bp variable TSDs. The individual copies have shown high homology (52–99%) in their entire lengths. The study revealed that the elements are less in numbers but active in Brassica rapa genomes and PCR amplification revealed their specificity and amplification in A-genome containing diploid and polyploids Brassica. The phylogenetic analysis of Brassica MULEs with other plant Mutator elements revealed that no correlation exists between Brassica MULEs and other elements suggesting a separate line of evolution. Analyzing the regions flanking the insertions revealed that the insertions have showed a preference for AT rich regions. The detailed study of these insertions revealed that although less in number and small sizes, they have played a role in Brassica genome evolution by their mobilization.

Key words: Transposable elements, Brassica, Mutator, Diversity, Shahroz, Phylogenetic analysis

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Intergeneric hybridisation between Berula erecta and Helosciadium nodiflorum (Apiaceae)

Intergeneric hybridisation in the Apiaceae

Intergeneric hybridisation in the Apiaceae Desjardins et al. 2015

TS. Desjardins SD, Leslie AC, Stace CA, Schwarzacher T,  Bailey JP. 2015. Intergeneric hybridisation between Berula erecta and Helosciadium nodiflorum (Apiaceae). Taxon 64:
784-794. DOI: 10.12705/644.9 Publisher link££ Author version Intergeneric hybridisation

A hybrid between Berula erecta and Helosciadium nodiflorum is reported from Chippenham Fen National Nature Reserve (NNR), Cambridgeshire, England. Parentage was investigated using chromosome counts, a maternally-inherited chloroplast marker (rps16-trnK), a biparentally-inherited nuclear marker (the ITS), and fluorescent in situ hybridisation (FISH) using labelled total genomic probes. Two parental genomes were identified in the putative hybrid (2n = 20), a maternal genome consisting of 9 chromosomes from B. erecta (2n = 18) and a paternal genome consisting of 11 chromosomes from H. nodiflorum (2n = 22). The implication of this hybrid for the taxonomy of the group is discussed, and a new hybrid genus is described: x Beruladium A.C. Leslie (= Berula Besser ex W.D.J. Koch x Helosciadium W.D.J. Koch). In overall appearance the hybrid resembles a small, creeping H. nodiflorum, and can be identified in the wild by a combination of characters: 1) the absence of a ring-mark on the petiole below the lowest pair of leaflets that is characteristic of pure Berula, 2) lower leaves with up to 5 pairs of leaflets, 3) peduncles varying from shorter than to longer than rays, 4) umbels with several usually untoothed bracts, 5) a relatively long stigma and style, and 6) the absence of ripe fruits. The detection of this taxon is of considerable interest and, as far as we know, it is the first confirmed intergeneric hybrid in the Apiaceae within Europe.


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