FY2017 Annual Report

Evolutionary Genomics Unit
Assistant Professor Thomas Bourguignon

Back row, left to right: Taisuke Kanao, Tom Bourguignon, Lazzat Aibekova, Lucia Zifcakova, Yukihiro Kinjo.

Front row, left to right: Chihiro Arasaki, Menglin Wang, Jigyasa Arora, Crystal Clitheroe, Ales Bucek.

 

 

Abstract

The Evolutionary Genomics Unit was started in May 2017. We study the evolution and ecology of termites and cockroaches using high-throughput sequencing methods. Our main research areas presently include: the evolution of symbiosis between insects and bacteria, and the reconstruction of the insect tree of life. During the fiscal year 2017, we spent a lot of effort to settle the lab, and started generating our first results, as detailed hereunder. 

1. Staff

  • Dr. Thomas Bourguignon, Assistant Professor
  • Dr. Ales Bucek, Postdoctoral Scholar
  • Dr. Lucia Zifcakova, Postdoctoral Scholar
  • Crystal-Leigh Clitheroe, Research Unit Technician
  • Yukihiro Kinjo, Research Unit Technician
  • Jigyasa Arora, PhD Student
  • Menglin Wang, PhD Student
  • Chihiro Arasaki, Research Unit Administrator

2. Collaborations

2.1 Historical biogeography of termites

  • Type of collaboration: Joint research
  • Researchers:
    • Professor Yves Roisin, University of Brussels
    • Professor Nathan Lo, University of Sydney
    • Professor Rudolf A. Scheffrahn, University of Florida
    • Associate Professor Jan Sobotnik, Czech University of Life Sciences
    • Associate Professor Theodore A. Evans, University of Western Australia
    • Associate Professor David Sillam-Dusses, University of Paris 13

2.2 Functional evolution of termite gut microbes

  • Type of collaboration: Joint research
  • Researchers:
    • Professor Andreas Brune, Max Planck Institute for Terrestrial Microbiology
    • Professor Nathan Lo, University of Sydney
    • Associate Professor Jan Sobotnik, Czech University of Life Sciences

2.3 Evolution of cockroaches and their associated Blattabacterium

  • Type of collaboration: Joint research
  • Researchers:
    • Professor Gaku Tokuda, University of the Ryukyus
    • Professor Nathan Lo, University of Sydney

3. Activities and Findings

3.1 Historical biogeography of termites

The worldwide patterns of species distribution are shaped by historical and ecological factors. However, biogeographic studies rarely focus on ecology and history simultaneously to explain species distribution. We use genome and transcriptome-based phylogenies to resolve the distribution patterns of termites whose diversity and abundance vary along the unusual sequence Africa -> South America -> South East Asia -> Australia, and which are more common in the southern rather than northern hemisphere. Time-calibrated phylogenies inform on both the timing of dispersals, and on the directionality. Using this information, we can determine the ecological and historical factors responsible of the anomalous distribution patterns of termites, so well as determine how termites became the main decomposers in tropical ecosystems. During the fiscal year 2017, we prepared over 250 samples, each belonging to different termite species, for mitochondrial genome sequencing. 

3.2 Functional evolution of termite gut microbes

Termites harbor a large number of symbiotic microbes in their gut. Gut microbes provide their host with amino acids and vitamins and help digesting various types of organic matter, including wood, soil, and leaf litter. Few animal groups eat wood and soil, and how they evolved to do so is still largely unknown. As a first step, we studied the evolution of gut bacterial communities using 16S rRNA sequencing. This approach informed us about the evolution of bacterial communities. We then built molecular phylogenies with these 16S sequences, together with sequences from relatives found in other environments, which we obtain through BLAST search of the ncbi database. We found that the majority of termite-derived phylotypes form large monophyletic groups, indicating that termites and their gut microbes coevolve to a large extent, and that most termite gut bacteria are specialized to live in termite gut. However, we also found that numerous clades are interspersed with bacterial lineages from the gut of other animals, showing that horizontal transfers also shaped the termite gut bacterial communities. Overall, our results indicate that mixed-mode transmission, combining vertical and horizontal transfers, is shaping the gut microbiome of termites.

Because 16S rRNA sequencing provides no insight into the function carried out by gut microbes, we are now sequencing the gut metagenomes of a representative set of termite species.  During the fiscal year 2017, we started sequencing a total of 221 gut metagenomes. This dataset represents the first attempt to elucidate the functional evolution of the gut microbiome of an insect order. 

3.3 Evolution of cockroaches and their associated Blattabacterium

Many animals are associated with bacterial endosymbionts that participate to their metabolism. Endosymbionts have reduced genomes that evolve in absence of gene input from outside sources. We study the evolution of cockroaches, and the evolution of the genome of Blattabacterium, the endosymbiotic bacteria of cockroaches. During the fiscal year 2017, we prepared a phylogenetic tree, based on the mitochondrial genomes of 119 cockroach species, that partly resolved the relationships among the main cockroach lineages. We are now focusing on the evolution of the genome of the genomes of Blattabacterium. To do so, we obtain the full Blattabacterium sequence of 67 strains and, using phylogenetic trees, we will determine the pace of genome evolution during the last 220 million years of Blattabacterium-cockroach coevolution. 

 

4. Publications

4.1 Journals

  1. Bourguignon T*, Lo N* (*equal first authors), Dietrich C, Šobotník J, Sidek S, Roisin Y, Brune A, Evans TA. Rampant host-switching shaped the termite gut microbiome. Curr Biol, 28, 649-654. This article has been recommended in F1000Prime as being of special significance in its field.  doi: 10.1016/j.cub.2018.01.035 (2018)
  2. Bourguignon T, Dahlsjö CAL, Jacquemin J, Gang L, Wijedasa LS, Evans TA. Ant and termite communities in isolated and continuous forest fragments in Singapore. Insectes Soc, 64, 505-514. doi: 10.1007/s00040-017-0570-y (2017)
  3. Hamidi R, de Biseau J-C, Bourguignon T, Martins Segundo GB, Fontenelle MTB, Quinet Y. Dispersal strategies in the highly polygynous ant Crematogaster (Orthocrema) pygmaea Forel (Formicidae: Myrmicinae). PLoS One 12, e0178813. doi: 10.1371/journal.pone.0178813 (2017)
  4. Hellemans S, Bourguignon T, Kyjakova P, Hanus R, Roisin Y. Mitochondrial and chemical profiles reveal a new genus and species of Neotropical termite with snapping soldiers, Palmitermes impostor (Termitidae : Termitinae). Invertebr Syst 31(4):394-405. doi: 10.1071/Is16089 (2017)
  5. Scheffrahn RH, Bourguignon T, Bordereau C, Hernandez-Aguilar RA, Oelze VM, Dieguez P, Obotnik JS, Pascual-Garrido A. White-gutted soldiers: simplification of the digestive tube for a non-particulate diet in higher Old World termites (Isoptera: Termitidae). Insectes Soc 64(4):525-533, doi: 10.1007/s00040-017-0572-9 (2017)
  6. Palma-Onetto V, Hošková K, Křížková B, Krejčířová R, Pflegerová J, Bubeníčková F, Plarre R, Dahlsjö CAL, Synek J, Bourguignon T, Sillam-Dussès D, Šobotník J. The labral gland in termite soldiers. Biol J Linn Soc 123, 535-544, doi: 10.1093/biolinnean/blx162 (2018)

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

Nothing to report

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminars

1. Seminar by Dr. Taisuke Kanao, Graduate School of Human and Environmental Studies, Kyoto University
  • Title: Species diversity and evolution of termitophilous rove beetles
  • Date: November 7, 2017
  • Venue: OIST Campus Lab 3
2. Seminar by Dr. Nathan Lo, School of Life and Environmental Sciences, The University of Sydney
  • Title: Evolution of the termite gut microbiota
  • Date: January 11, 2018
  • Venue: OIST Campus Lab 3
3. Seminar by Dr. Theodore Evans, The Western University of Australia
  • Title: Evolution of the termite 'worker' phenotype: a reinterpretation of observations and reconsideration of hypotheses
  • Date: January 23, 2018
  • Venue: OIST Campus Lab 3

7. Other

Nothing to report.