Evo-devo themed Phil Trans issue out

Cheryll Tickle and Araxi Urrutia have put together a themed Phil Trans B issue on evo-devo research. There is a broad selection of papers, mainly on animal evolution and development, but there are also two on plant evo-devo.

My review covers genetic and developmental changes in the radiation of plant body plans, and will be useful to undergraduate and palaeo MSc students at Bristol taking the ‘flowering plants’ module. The Soltis lab reviews the evolution of floral diversity.

Cheryll and Araxi have written an interesting overview of the issue including perspectives on the history and goals of evo-devo research and the current state of play.

You can access the papers here.

Paper on liverwort shape out

Thanks to Anne Knowlton and Current Biology for working with us get the first paper from Jeremy Solly’s PhD out, now online here :-).

In it we address the question of how plant shape arises in an ancient planar growth form, the liverwort thallus. We have found that growth rate variation is sufficient to determine thallus shape, and that auxin production in the notch region is likely to pattern growth rate variation.

In contrast, planar shapes in flowering plants emerge by differential growth oriented with respect to each cell’s internal compass, or polarity. The results raise questions about the roles of polarity in liverwort thalli and how the mechanisms that determine plant shape have changed through evolution.

Comparing liverwort and flowering plant development spans the broadest evolutionary distance in land plants, so if we identify shared mechanisms for shape in the future, they are likely to have broad relevance to future efforts to engineer shape.

Review on the evolution of branching forms out, and the evolution of stomata.

I have had a small review on the evolution of branching forms published in New Phytologist. You can read the article here.

I greatly enjoyed examining Bobby Caine's PhD thesis in Sheffield on Friday. He has two lovely papers out on the evolution of genetic networks for stomatal development, one on the bHLH transcription factors that are necessary for stomata development in Physcomitrella, and one on the mechanisms that pattern Physcomitrella stomata. There should be more on the way too!

Paper accepted and paper out

Jeremy Solly, Nik Cunniffe and I have written up part of Jeremy's PhD research on mechanisms for shape determination in the liverwort Marchantia polymorpha.

We have used a combination of developmental, statistical, computational and pharmacological approaches to address the problem, and the results will be published soon in Current Biology.

Results from Ross Dennis's work in my lab and Paolo Bombelli's work in Chris Howe's lab in Cambridge are now published in Royal Society Open Science.

In it we show that mosses can be grown in waste tip boxes to convert them into fuel cells with sufficient output to power a small radio or environmental sensor, and bacterial contaminants that grow happily with the moss boost the power output.

Congrats to Jeremy and Ross!

PhD opportunity: Mechanisms for shape determination in Marchantia polymorpha

Project description:

Plant shapes range from tiny string or mat-like forms to massive multilayered upright forms with complex organ systems such as shoots, roots and leaves. Despite these wide differences in shape, many plant gene families are very ancient, predating diversification. We can therefore study the mechanisms for shape determination in simple plants such as liverworts and use the knowledge gained to understand plant shape determination in general.

To this end, my lab has used a combination of live imaging, statistical model fitting, computational modeling and molecular biology to discover mechanisms regulating shape in the liverwort Marchantia polymorpha.

We found that Marchantia undergoes a stereotypical sequence of shape transitions during development. Key aspects of global shape depend on regional growth rate differences specified by the co-ordinated activities of the growing apical notches. Using modelling we show that a diffusible growth promoting morphogen produced at each notch cannot fully account for the observed growth rate distributions. Instead, we hypothesize that the notches may pre-pattern the growth rate distribution. Your project will build on our prior work to validate the above ‘notch pre-patterns growth’ model of shape determination to discover the molecular identities of factors contributing to growth.

The project aim is to test the hypothesis that the plant hormone auxin corresponds to the notional morphogen in our ‘notch pre-patterns growth’ model of shape determination.

The project will involve:

1.          Analysis of the auxin distribution in Marchantia polymorpha

2.          Up and down regulation of auxin biosynthesis, transport, conjugation and decay

3.          Analysis of mutant shapes using live-imaging

4.          Comparison between experimental manipulations and model manipulations.

Training:

By combining computational and wet lab approaches, the project will provide training at the cutting edge of the plant evolution and development fields. The techniques that you learn will be broadly applicable in the academic biology and biotech sectors. The skills that you learn will be widely transferable to other areas such as science policy, publishing and computing.

Further information:

Please contact Dr Jill Harrison (jill.harrison@bristol.ac.uk) for further information about the project and application procedures.

NERC PhD studentship available: Body plan evolution in plants

Supervisors: Dr Jill Harrison, University of Bristol (main supervisor); Dr Tom Williams, University of Bristol; Dr Gary Barker, University of Bristol
 

A range of multicellular plant forms.

Plants and animals both evolved complex multicellular forms from a unicellular ancestor shared around 1.6 billion years ago. Whilst animal body plans are determined by cell shape, adhesion and movement during embryo development, plant cells cannot move and body plans are instead determined by cell division and growth throughout development [1]. Plant body plans range from tiny string or mat-like forms that grow across a surface to massive multilayered upright forms with complex organ systems such as shoots, roots and leaves. Despite these wide differences, many of the gene families involved are very ancient, predating the radiation of plant body plans. This raises questions about the nature of genetic change driving body plan innovations.

For the first time, new model systems across the plant tree of life have opened the possibility of identifying the genes involved in plant evolution [2]. To date this has been done by transferring knowledge of flowering plant development to other species on a gene-by-gene basis. However, this approach is biased and places undue weight on the knowledge that we already have.

This project aims to use novel bioinformatic approaches [3,4] to unlock plant body plan evolution by wholesale, genome-wide identification of genes associated with specific innovations.

The project will involve:

1.     Plant collection and growth

2.     DNA extraction, genome sequencing and genome annotation

3.     Data mining and bioinformatic analysis

4.     Targeted analyses of gene function.

Whilst animal body plans radiated in Cambrian seas, plant body plans radiated on land during the Devonian era. Results from your project will pinpoint the genetic changes that generated the terrestrial biosphere.

By combining distinct bioinformatic and wet lab skill sets, the project will provide training at the cutting edge of the plant evo-devo field. The techniques you learn will be broadly applicable in academic biology and biotech sectors. The skills you learn will be widely transferable to other areas such as science policy, publishing, computing and finance.

Application: The scholarship is open to UK and EU applicants, and the deadline is 6 January 2017. The application form and guidelines are available here at the address below:

http://www.bristol.ac.uk/study/postgraduate/apply/

Further information:

Please see http://www.bristol.ac.uk/biology/people/jill-j-harrison/index.html or e-mail Jill Harrison (jill.harrison@bristol.ac.uk) with any questions about the project or for access to the papers below.

Further reading:

[1] Meyerowitz EM (2002). Plants compared to animals: the broadest comparative study of development. Science 295: 1482-148.

[2] Harrison CJ (2016). Developmental and genetic changes in the evolution of land plant body plans. Accepted for publication in Phil Trans R Soc B.

[3] Szöllősi GJ et al. (2013). Efficient exploration of the space of reconciled gene trees. Syst Biol 62: 901-912.

[4] Williams et al. (2015) New substitution models for rooting phylogenetic trees. Phil Trans R Soc B 20140336.

Two papers accepted

Jill Harrison has had a review paper on auxin transport in the evolution of branching forms accepted for publication as a Tansley Insight in New Phytologist.

In a second paper, Paolo Bombelli, Ross Dennis and co-author use Physcomitrella patens in a simple fuel cell with sufficient output to power a commercial radio receiver or LCD desktop weather station. The results will be published in Royal Society Open Science.

Congratulations to Stephanie Sang!

Congratulations to Stephanie Sang who has been awarded travel funding to attend the EuroEvoDevo meeting in Uppsala next week. She will be presenting an expression analysis of CLAVATA pathway components in Physcomitrella.

Congratulations also for receipt of the Programme Director’s Commendation for excellent coursework.

And many thanks for the delicious scones and cream :-).

Transcriptome data from three rare plants at key phylogenetic nodes.

Kingsley Dixon¹, Jill Harrison², Sandy Hetherington³, Joshua Mylne⁴ and Jingling Zhang⁴.

1.  Kings Park Science, Botanic Gardens and Parks Authority, Fraser Avenue, Perth 6005, Australia

2.  School of Biological Sciences, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.

3.  Plant Sciences Department, South Parks Road, Oxford, OX2 3RB, UK

4.  The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia.

In October 2014 we reported transcriptome sequencing for the lycophytes Phylloglossum drummondii and Isoetes drummondii and the basal angiosperm representative Trithuria bibracteata (Figure 1) in a blog post (DOI: 10.13140/RG.2.1.4814.7445). We envisaged that sequence data would be useful for gene discovery in systematic and evo-devo studies due to the paucity of sampling in these lineages and their key taxonomic position. Some technical glitches gave a delay in obtaining high quality RNA, but this has now been overcome and the data are available from joshua.mylne@uwa.edu.au.

Figure 1: Phylloglossum drumondii, Isoetes drummondii and Trithuria bibracteata samples used in RNA extraction.

RNA was extracted using a phenol and lithium chloride prep followed by a NucleoSpin clean up. Sequencing libraries were generated from 300-1000 ng of purified total RNA using the TruSeq® Stranded Total RNA LT with Ribo-Zero Plant kit (Illumina). Approximately 100 million paired-end 151 bp Illumina raw reads were acquired for each species. Jingjing Zhang assembled the transcriptomes as described by Jayasena et al. (2014) using approximately 70 million clean reads for each species. Assemblies were done four times for each species using a different word size setting in CLC Genomics (20, 30, 40 and 60). The number of contigs assembled per transcriptome ranged from approximately 140,000-150,000 for word size 20 to 200,000-250,000 for word size 60.

Sandy Hetherington has undertaken a preliminary phylogenetic analysis of KNOX homeodomain genes demonstrating data utility by the expected placement of gene homologues (Figure 2). The 30 word sized transcriptome assemblies were used for the analysis. Protein coding regions were predicted using GeneMarkS-T (Tang et al 2015). KNOX sequences were identified by a BLAST search with a query of KNOX proteins from; Arabidopsis thaliana (At), Oryza sativa (Os), Selaginella moellendorffii (Sm), Physcomitrella patens (Pp), Chlamydomonas reinhardtii (Cr), Ostreococcus tauri (Ot) based on the analysis by Mukherjee and colleagues (2006). Proteins were aligned using MAFFT (Katoh and Frith 2012) and manually trimmed using Bioedit (Hall, 1999) to the 64 amino acids that constitute the conserved homeodomain. A maximum likelihood phylogenetic analysis was carried out in RAxML (RAxML version 8.0.5) (Stamatakis, 2014), protein model PROTGAMMAAUTO and 1000 rapid bootstraps. The phylogenetic analysis was rooted on the closely related Arabidopsis BEL protein At_BEL1.

Figure 2: ML tree showing position of Phylloglossum drummondii (Pd), Isoetes drummondii (Id) and Trithuria bibracteata (Tb) contigs identified from transcriptomes.

We hope that the data will be useful to the evo-devo community and encourage potential users to get in touch with Josh for access.

References:

Hall T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.

Jayasena A. S., Secco D, Barnath Levin K., Berkowitz O., Whelan J. and Mylne, J. 2014. Next generation sequencing and de novo transcriptomics to study gene evolution. Plant Methods. DOI: 10.1186/1746-4811-10-34

Katoh K, Frith MC. 2012. Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics 28: 3144–3146.

Mukherjee K, Brocchieri L, Bürglin TR. 2009. A comprehensive classification and evolutionary analysis of plant homeobox genes. Molecular Biology and Evolution 26: 2775–2794.

Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.

Tang S, Lomsadze A, Borodovsky M. 2015. Identification of protein coding regions in RNA transcripts. Nucleic Acids Research 43: 1–10.

Paper accepted and lab comings and goings

Jill Harrison has had a review article accepted for the upcoming Philosophical Transactions of the Royal Society B volume on ‘Evo-devo in the genomics era and the origins of morphological diversity’.

Yoan Coudert has left the lab to start up his own group as CNRS ATIP Research Fellow at the Muséum National D’Histoire Naturelle in Paris. Building on our eLIFE (2015) paper, Yoan will be looking into the diversification of branching forms in mosses.

Stephanie Sang has joined the lab from the Bristol Palaeobiology MSc course and is looking into CLAVATA gene function in the moss, Physcomitrella patens. She will be presenting her results at the ‘Euro Evo-Devo 2016’ meeting in Uppsala before writing up her thesis and returning to the US to start her PhD rotations at the University of Chicago.

Zoe Nemec-Venza will be joining the lab as a Sainsbury Student in October 2016 from a Masters course at the University of Pisa.

Our small group will welcome new applicants to the lab!

Source files for BG trail....

Are saved as illustrator files on Google Drive and can be downloaded from this  link.... (Now adapted to Bristol Botanic Garden).