CAFE: a computational tool for the study of gene family evolution

Bie, Tijl De; Cristianini, Nello; Demuth, Jeffery P.; Hahn, Matthew W.

doi:10.1093/bioinformatics/btl097

Cited by 1,438 publications

(1,234 citation statements)

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“…The abundance and types of these enzymes should be key to the adaption to different host-based nutrition. The expansion and contraction of CAZymes and MEROPS, as key enzymes responsible for substrate utilisation, were detected by the programme CAFÉ (Figure 4, Table S5) (De Bie et al 2006; Rawlings et al 2006; Cantarel et al 2009). One significant gene family contractions occurred during the divergence of animal pathogens in Cordycipitaceae with 101 contracted families of CAZymes and 29 of MEROPS.…”

Section: Resultsmentioning

confidence: 99%

“…Fungal secondary metabolite pathways were analysed with the program SMURF (http://www.jcvi.org/smurf/index.php). The evolution of the protein family sizes and expansion and contractions were analysed by CAFE (De Bie et al 2006). Simple repeat and transposable elements (TEs) were annotated using BLAST against the RepeatMasker library (http://www.repeatmasker.org/) (Tempel 2012).…”

Section: Methodsmentioning

confidence: 99%

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Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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“…T. urticae (Arachnida) was used as an outgroup, and a bootstrap value was set as 1000. In addition, the evolutionary changes in the protein family size (expansion or contraction) were analysed using the CAFÉ program 63 , which assesses the protein family expansion or contraction based on the topology of the phylogenetic tree.…”

Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.

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“…OrthoMCL clustered a total of 968 single-copy gene families, which were subjected to phylogenetic analyses by Mrbayes 54 . The expansion and contraction of the gene clusters were determined by a CAFE calculation (version 2.1) 55 on the basis of changes in gene family size in generated phylogenetic history. …”

Section: Competing Financial Interestsmentioning

confidence: 99%

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

et al. 2013

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l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...

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CAFE: a computational tool for the study of gene family evolution

Cited by 1,438 publications

References 4 publications

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

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