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).

Evolution trail goes live at CUBG

As an impact activity associated with my BBSRC grant 'PIN proteins and architectural diversification in plants' (BB/L00224811), I have worked with Dr Alison Murray (CUBG) and Prof Beverley Glover (CUBG and Plant Sciences Department, Cambridge University) to establish an evolution trail in the Cambridge University Botanic Garden.

The trail currently comprises a selection of plants chosen to represent key steps in plant evolution mapped out in the Garden with a handout to be used by undergraduates taking the 'evolution and behaviour' module that can be signed out from the Brookside entrance.

The trail handout can be downloaded here.

New interpretation boards to showcase the relevance of plants in the 'life before flowers' greenhouse have been designed and will be produced in 2016.

The trail conveys ideas about how plant life has changed over geological timescales from the time that tiny bryophyte-like plants first started to colonise land, through the establishment of the earliest vascular plant shooting systems to the radiation of today's dominant flowering plant flora.

The conquest of land by plants cooled the earth's climate, established the first soils, and provided the food and shelter that allowed animals to colonise land.

Recurring themes of plant interrelationships, plant adaptation to new environments and plants shaping their environment have great relevance to future challenges to humanity in the face of rapid population growth and climate change.

Congratulations to Jeremy Solly!

Jeremy had his PhD viva on the 6th of November in Cambridge, and has passed with minor corrections.

His work aimed to determine how growth dynamics contribute to overall plant shape in the liverwort Marchantia polymorpha. He has used  live-imaging, growth analysis, and predictive computational modelling in combination with surgical, pharmacological and genetic manipulations.

His work suggests a model of growth whereby the apical notches regulate shape by setting regional growth rate differences across the thallus, and we are hoping to publish the results soon!

Jeremy has now embarked on a third degree to train as a medical doctor.

Sainsbury funded 4-year PhD studentship available

The evolution of plant body plans

The conquest of land by plants over 450 million years ago was one of the most significant events in our planet's history, and was underpinned by a series of key innovations in plant architecture during evolution1.

Our group aims to identify the developmental and genetic basis of two such innovations, three dimensional shoot growth and branching2,3, in a range of model systems representing different stages of plant evolution.

Our recently published work reports mutants with disrupted branching patterns in a moss3-6 and ongoing work has identified mutations that disrupt 3D growth.

Your project will build on these advances to identify molecular determinants of body plan in early diverging land plant lineages.

For further information please see the Harrison lab web page (http://www.bristol.ac.uk/biology/people/jill-j-harrison/overview.html) or contact Dr Harrison directly to discuss your ideas (jill.harrison@bristol.ac.uk).

After discussion, applicants should be prepared to supply a 2-page research proposal, a CV and an academic transcript including the names of three referees. 

The deadline is January 20th 2016.

International students are welcome to apply. 

Further information:

Gatsby

Nature jobs

Further Reading:

[1] Pires and Dolan (2012). Morphological evolution in land plants: new designs with old genes. Phil. Trans. R. Soc. 367: 508-518.

[2] Olsen et al 2015 DEK1; missing piece in puzzle of plant development Trends in Plant Science 20: 70-71.

[3] Harrison CJ. 2015. Shooting through time: new insights from transcriptomic data. Trends in Plant Science. DOI:10.1016/j.tplants.2015.06.003.

[4] Coudert YN, Palubicki W, Ljung K, Leyser O, and Harrison CJ. Three ancient hormone pathways regulate shoot branching in a moss. eLife 4 e06808.

[5] Bennett et al. (2014a). Plasma membrane targeted PIN proteins regulate shoot development in a moss. Current Biology 24: 1-10.

[6] Bennett et al. (2014b). Paralogous radiations of PIN proteins with multiple origins of non-canonical PIN structure. Molecular Biology and Evolution (doi:molbev.msu147).