Format

Send to

Choose Destination
BMC Genomics. 2019 Jun 12;20(1):485. doi: 10.1186/s12864-019-5680-7.

Evolution and comparative genomics of the most common Trichoderma species.

Author information

1
Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.
2
, Vienna, Austria.
3
Departamento de Biologia Celular, Universidade de Brasília, Brasíla, DF, Brazil.
4
US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
5
Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Naples, Portici, Italy.
6
CNRS, Aix-Marseille Université, Marseille, France.
7
INRA, Marseille, France.
8
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
9
Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
10
Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España.
11
Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
12
Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China. qirongshen@njau.edu.cn.
13
US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. ivgrigoriev@lbl.gov.
14
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA. ivgrigoriev@lbl.gov.
15
Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria. Irina.druzhinina@njau.edu.cn.
16
Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China. Irina.druzhinina@njau.edu.cn.

Abstract

BACKGROUND:

The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood.

RESULTS:

We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function.

CONCLUSIONS:

Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.

KEYWORDS:

Ankyrin domains; CAZymes; Core genome; Environmental opportunism; Gene gain; Gene loss; Orphans; SSCPs

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center