Plant Virus Evolution and Pararetroviruses in Petunia

Plant Pararetrovirus insertions on chromosomes seen on the cover of "Plant Virus Evolution" book

Plant Pararetrovirus insertions on chromosomes seen on the cover of “Plant Virus Evolution” book

TS. Hohn T, Richert-Pöggeler KR, Staginnus C, Harper G, Schwarzacher T, Teo CH, Teycheney P-Y, Iskra-Caruana M-L, Hull R. 2008. Evolution of Integrated Plant Viruses. Chapter 4 pp 53-81. In: Plant Virus Evolution Ed Roossinck MJ. Springer: Berlin

Link to Publisher homepage about the book with links to downloadable copies of the whole book or the chapter.

(Freely downloadable direct links do not seem to work except via the page above: PRV Pararetrovirus chapter or as the whole book”Plant Virus Evolution” 4Mb.)

This volume has just become free on-line. Despite being 7 years old, it had enough genomic information that the pararetrovirus (EPRV Endogenous Para Retro Virus) chapter is still current in 2015. It also foreshadowed the Journal papers linked via Google Scholar at the bottom of this page.

Plant pararetroviruses replicate their genome via a transcription–reverse transcription cycle like retroviruses, but unlike them their genomes do not obligatorily integrate into the host chromatin. Nevertheless, one can find complete or fragmented pararetrovirus PRV EPRV genomes, as well as those from geminiviruses and even RNA viruses incorporated into the genomes of nearly all plants analysed. Integration events are thought to be rare and even rarer are those that find their way into the germ line. Normally, these integrated viral sequences are incomplete, rearranged and mutated and cannot easily escape as active viruses. However, in some cases apparently more recently acquired and therefore less initiated integrates can escape by direct transcription from tandem insertions or by recombination. This can lead to severe outbreaks in crop and ornamental plants. In anticipation of such events, methods have been developed for the detection and characterization of integrated virus sequences in plant genomes.

See more recent journal articles on PRVs EPRVs relating to the work overviewed in this chapter

[HTML] Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species

…, MLC Machado, M Matzke, T Schwarzacher – BMC plant …, 2007 –
How Teo 4 , Eduviges Glenda Borroto-Fernández 5 , Margit Laimer da Câmara Machado 5 , Although EPRVs are being detected in an increasing number of plant species, the detailed structure of individual EPRV integrants and

Fluorescent in situ hybridization to detect transgene integration into plant genomes

T Schwarzacher – Transgenic Wheat, Barley and Oats, 2009 – Springer
Wild Petunia metaphase chromosomes (2 n = 14) after FISH with an endogenous pararetrovirus, EPRV probe (labelled with biotin d-UTP and detected with streptavidin conju- gated to Alexa594, red fluorescence under green excitation (for probe description ..

Impact of Retroelements in Shaping the Petunia Genome

KR Richert-Pöggeler, T Schwarzacher – Petunia, 2009 – Springer .. Evidence accumulated so far indicates that integration of EPRV into the plant genome does not occur actively but as a by  form higher-order repetitive DNA structures that are amplified by mechanisms of repetitive sequence amplification






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Descriptors for Crocus (Crocus spp.)

Descriptors for Crocus species morphology

Descriptors for Crocus species morphology

312. Molina RV, Guardiola JL, García-Luis D, Renau-Morata B, Sanchis E, González-Nebauer S, de los Mozos M, Rodríguez-Conde MF, Santana O, Pastor-Férriz MT, Fernández JA, Santaella M, Roldán M, Tsimidou M, Polissiou M, Heslop-Harrison JS, Branca F, Mathew B. 2015. Descriptors for Crocus (Crocus spp.). 74pp. Bioversity International, Rome. ISBN-13: 978-92-9043-999-8

Full document:

Abstract and summary:

Conservation of saffron and allies is particularly concerning because of the shrinking of their populations both in the wild and in cultivated areas. In this regard, the descriptors developed for these species represent a valuable instrument for a better comprehension of these dwindling resources in support of their enhanced conservation and use and following the international agreed protocol of Bioversity International. A list of descriptors based on evaluation studies carried out on saffron and Crocus accessions and taking into account taxonomic criteria for this genus have been developed within the framework of the EU funded Programme AGRI GEN RES, (Action 018,, coordinated by the Universidad de Castilla-La Mancha (Spain). One of the main achievements of this Programme has been the creation of the World Saffron and Crocus Collection, maintained by the Bank of Plant Germplasm of Cuenca, which belongs to the Junta de Comunidades de Castilla – La Mancha (Spain).

The Crocus genus is part of the Iridaceae family and consists of more than 88 corm-bearing perennial species distributed from Central and Southern Europe, to North Africa, Southwest Asia and Western China, with the centre of species diversity located in Asia Minor and the Balkan Peninsula (Mathew 1982; Goldblatt et al., 2008; Petersen et al., 2008; Harpke et al., 2013). Many Crocus species are highly appreciated as garden plants for their colourful flowers, but the genus is mainly known for the species C. sativus, commercially cultivated for the production of saffron, the world’s most expensive spice (Fernández 2004). Saffron has been widely known since the pre-Hellenic and Hellenic periods.

Download full book from:

Download webpage with abstract, background and summary with link to full book:

Local copy of book: Descriptors for Crocus species morphology

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Diversity and characters in Ethiopian linseed Linum #PAGXXIII Negash Worku

Worku looking at linseed Linum trails in Ethiopia

Worku looking at linseed Linum trails in Ethiopia

Many people have talked about Orphan crops – those where there has been little genetic or other research – and the characterization, evaluation and exploitation of germplasm at the #PAGXXIII Plant and Animal Genome Conference this week. Today, I am talking about work by Negash Worku on the Diversity and Characters in Ethiopian Linseed Accessions. SLIDES BELOW!

Ethiopia is a centre of diversity for linseed, where it is valued for cultural reasons as well as use as food and for export. Limited amounts of the crop are grown widely in Ethiopia, which includes the unique climatic conditions of the tropical highlands (3-15°N, >2000m). A range of some 200 accessions were evaluated for diverse quality, agronomic and morphological traits. They were also genotyped with IRAP (InterRetroelement Amplified Polymorphisms). It is probable that the genetic diversity in this area has not been exploited in breeding programmes. The results show a range of characters which can be exploited, some appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs. Analysis of sequence data is likely to allow identification of probes suitable for chromosome identification and potentially tracking chromosomes in breeding programmes.

The slides are on Slideshare,

Linked here on there is a preprint of the first paper reporting this work.

Our work with Ethiopian germplasm and the farmer-led trials is overviewed here.

A related post on food security, our interests and needs in water usage and drought is here.


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Transposable Elements in the Musa and Banana Genome: PAGXXIII conference talk

There has been a lot of talk about transposable elements during the Plant and Animal Genome #PAGXXIII meeting this week. As half or more – often 75% – of all the DNA in a plant or animal genome is typically made of class I retrotransposons and class II DNA transposons, this widespread interest is right! My own talk at the Banana genomics session, now live on Slideshare, was one of many of the transposon talks. I focussed on a class of DNA elements, the hAT transposons, where the abundance, diversity and chromosomal localization has not been studied in detail in many species where the hAT elements and their derived MITEs with the major gene deleted. The talk is here:

It overviews our work on transposable elements in the Musa or banana genome, using genomic sequence, bioinformatics, diversity panels and in situ hybridization approaches.

References to the work are given at the end of the slideshare.


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2014 in review: Molecular cytogenetics website activity

The stats helper monkeys prepared a 2014 annual report for this blog. Obviously, my New Year’s Resolution must be to put more of the things I do onto the website, and not have such long gaps. Of course, half-a-dozen posts of more general interest was also put onto and I’ll be planning to post more there as well!

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 9,500 times in 2014. If it were a concert at Sydney Opera House, it would take about 4 sold-out performances for that many people to see it.

Click here to see the complete report.

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Diversity in Ethiopian linseed (Linum usitatissimum): morphology and seed oil

Linseed morphological variation. Negash et al. 2015 GRACE Genet Res Crop Evol

Linseed morphological variation. Negash Worku et al. 2015 GRACE Genet Res Crop Evol

Worku N, Heslop-Harrison JS, Wakjira A. 2015. Diversity in 198 Ethiopian linseed (Linum usitatissimum) accessions based on morphological characterization and seed oil characteristics. Genetic Resources and Crop Evolution (GRACE) in press Dec 2014. doi:10.1007/s10722-014-0207-1 (on-line 20 Jan 2015). And Worku: Linum / Linseed Morphological Diversity in Ethiopia – Author Version.

Morphological and molecular characterization of germplasm is important for the sustainable exploitation of crops. Linseed or flax (Linum usitatissimum L.) is a multipurpose crop grown in many environments for food, feed, fibre and industry. In Ethiopia, a centre of diversity for linseed, it is valued for food and export. Here, we aimed to develop and use a set of morphological descriptors to determine levels and patterns of diversity in Ethiopian germplasm from the tropical highlands (3-15°N, >2000 m a.s.l.) in 198 Ethiopian traditional varieties. The Ethiopian traditional varieties included plants with both fibre and oil-seed stem-branching morphotypes, although most were relatively small-seeded. Traditional variety oil quality was assessed; oil content was as low as 30% compared to 47% reported elsewhere. Days-to-flowering and days-to-maturity varied widely and were highly heritable. Ethiopian linseed had dominant and recessive yellow seed genotypes; some had a recessive twinned or conjoined-seed character. The descriptors developed here will be useful for genetic mapping and selection of breeding lines. The results show the range of characters which can be exploited in breeding lines appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs.

And Worku: Linum / Linseed Morphological Diversity in Ethiopia – Author Version.

See also related post: about the trials.

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The diversification and activity of hAT transposons in Musa genomes

Musa hAT element organization, abundance and phylogeny. Menzel et al. Chromosome Research 2015

Musa hAT element organization, abundance and phylogeny. Menzel et al. Chromosome Research 2014

Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoerme M, Heslop-Harrison JS, Schmidt T. 2014. The diversification and activity of hAT transposons in Musa genomes. Chromosome Research 22: 559–571. DOI 10.1007/s10577-014-9445-5 and Pubmed link ID: 25377178 And author print hATs in Musa _2014_CR_MenzelEtAlAuthorVersion2014.

Sequencing of plant genomes often identified the hAT superfamily as largest group of DNA transposons. Nevertheless, detailed information on the diversity, abundance and chromosomal localization of plant hAT families are rare. By in silico analyses of the reference genome assembly and BAC sequences, respectively, we performed the classification and molecular characterization of hAT transposon families in Musa acuminata. Musa hAT transposons are organized in three families MuhAT I, MuhAT II and MuhAT III. In total, 70 complete autonomous elements of the MuhAT I and MuhAT II families were detected, while no autonomous MuhAT III transposons were found. Based on the terminal inverted repeat (TIR)-specific sequence information of the autonomous transposons, 1722 MuhAT I- and MuhAT II-specific miniature inverted repeat transposable elements (MuhMITEs) were identified. Autonomous MuhAT I and MuhAT II elements are moderately abundant in the sections of the genus Musa, while the corresponding MITEs exhibit an amplification in Musa genomes. By fluorescent in situ hybridization, autonomous MuhAT transposons as well as MuhMITEs were localized in subtelomeric, most likely gene-rich regions of M. acuminata chromosomes. A comparison of homoeologous regions of M. acuminata and Musa balbisiana BACs revealed the species-specific mobility of MuhMITEs. In particular, the activity of MuhMITEs II showing transduplications of genomic sequences might indicate the presence of active MuhAT transposons, thus suggesting a potential role of MuhMITEs as modulators of genome evolution of Musa.

Keywords Musa acuminata, Musa balbisiana, genome assembly, BAC, hAT transposons, FISH

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