OMA standalone: orthology inference among public and custom genomes and transcriptomes

Altenhoff, Adrian M.; Levy, Jeremy; Zarowiecki, Magdalena; Tomiczek, Bartłomiej; Vesztrocy, Alex Warwick; Dalquen, Daniel A.; Müller, Steven; Telford, Maximilian J.; Glover, Natasha; Dylus, David; Dessimoz, Christophe

doi:10.1101/gr.243212.118

Cited by 135 publications

(130 citation statements)

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“…To examine gene families that may have undergone expansions in association with functional divergence and specialization, we identified groups of orthologous genes that have increased and decreased in size in the two genomes, relative to one another. We identified these species-specific gene-family expansions using the Orthologous MAtrix (OMA) standalone package [74]. OMA predicted 8817 OMA groups (strict 1:1 orthologs) and 8578 Hierarchical Ortholog Groups (HOGs, Additional file 8).…”

Section: Gene Family Expansionsmentioning

confidence: 99%

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

et al. 2020

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Background: Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results: We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions: These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

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Section: Gene Family Expansionsmentioning

confidence: 99%

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

et al. 2020

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“…(a) We inferred a set of markers by running the OMA standalone algorithm 92 on a set of 149 archaeal genomes chosen to represent known taxonomic diversity. We inferred single protein trees for 97 orthologues that were present in at least 75% of the genomes and manually inspected the resulting trees to identify and remove 15 markers that had undergone gene transfer, resulting in a final set of 82 candidate single-copy orthologs.…”

Section: Methodsmentioning

confidence: 99%

Undinarchaeota illuminate the evolution of DPANN archaea

Dombrowski

Williams

Sun

et al. 2020

Preprint

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14 15 #corresponding author. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: anja.spang@nioz.nl. Phone16 number: +31 (0)222 369 526 17 18 19Several recent studies have revealed the presence of a thus far uncharacterized archaeal lineage 77 referred to the Uncultivated Archaeal Phylum 2 (UAP2) 13,40,41 , which seems to affiliate with DPANN 78 archaea and thus may be key in resolving long-standing debates regarding archaeal phylogeny and the 79 evolution of DPANN. In this study, we have used a metagenomics approach to obtain additional genomes 80 of members of the so far uncharacterized UAP2 and provide first insights into their metabolic repertoire 81 and lifestyle. Furthermore, we implemented comprehensive and careful phylogenomic techniques aimed 82 at ameliorating phylogenetic artifacts, shedding new light onto the evolutionary origin and phylogenetic 83 placement of the various DPANN lineages including UAP2 in an updated archaeal phylogeny. 84 Results and Discussion 85A thus far uncharacterized putative archaeal phylum-level lineage in metagenome read archives 86The generation of a large diversity of metagenome-assembled genomes (MAGs) representing 87 archaeal and bacterial lineages across the tree of life has led to the definition of the tentative archaeal 88 UAP2 phylum 41 . Considering our lack of insights into the biology of members of this lineage as well as its 89suggested key position in the archaeal tree, we aimed at obtaining a broader genomic representation of 90 the UAP2. In particular, we screened publicly available metagenomes using ribosomal protein sequences 91 of the previously reconstructed UAP2 MAGs and assembled and binned UAP2-positive samples yielding 92 six additional MAGs belonging to the UAP2 lineage (Table 1, Supplementary Tables 1-2, see Methods for 93 details). Four of the newly assembled MAGs were recovered from metagenomes of a groundwater aquifer 94 located adjacent to the Colorado River 42 , while the two others as well as six previously reconstructed 95MAGs, derived from metagenomes of marine waters in the Atlantic 41,43 and Indian Oceans 44 as well as the 96Mediterranean Sea 45 (Supplementary Table 2). UAP2 representatives were detected in samples from 97 various depths in the water column (85-5000 m), fluctuating oxygen conditions (anoxic to oxic) and 98 temperatures (sampling sites had temperatures from 18 up to 106°C) (Supplementary Figure 1, 99

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“…It is suggested that the hypothesized lineage of the cutinase gene emerged after its transference between distantly related plant-degrading microbes through lateral gene transfer events (LGTs) (Belbahri et al, 2008). Genes that evolved from what is considered to be an "ancient" duplication event (i.e., duplication before speciation as in the case of Pzezizomycotina and subsequent speciation events that occurred after a single duplication event) may have diverged to an extent that created new functions (Altenhoff et al, 2019).…”

Section: Orthologue Detection In 200 Fungal Genomes and Implicationmentioning

confidence: 99%

Diversity, structure, and synteny of the cutinase gene ofColletotrichumspecies

Villafana

Rampersad

2020

Ecology and Evolution

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Colletotrichum species complexes are among the top 10 economically important fungal plant pathogens worldwide because they can infect climacteric and nonclimacteric fruit at the pre and/or postharvest stages. C. truncatum is the major pathogen responsible for anthracnose of green and red bell pepper fruit worldwide. C. brevisporum was recently reported to be a minor pathogen of red bell pepper fruit in Trinidad, but has recently been reported as pathogenic to other host species in other countries. The ability of these phytopathogens to produce and secrete cutinase is required for dismantling the cuticle of the host plant and, therefore, crucial to the necrotrophic phase of their infection strategy. In vitro bioassays using different lipid substrates confirmed the ability of C. truncatum and C. brevisporum isolates from green and red bell peppers to secrete cutinase. The diversity, structure and organization and synteny of the cutinase gene were determined among different Colletotrichum species. Cluster analysis indicated a low level of nucleotide variation among C. truncatum sequences. Nucleotide sequences of C. brevisporum were more related to C. truncatum cutinase nucleotide sequences than to C. gloeosporioides. Cluster patterns coincided with haplotype and there was evidence of significant positive selection with no recombination signatures. The structure of the cutinase gene included two exons with one intervening intron and, therefore, one splice variant. Although amino acid sequences were highly conserved among C. truncatum isolates, diversity “hot spots” were revealed when the 66‐amino acid coding region of 200 fungal species was compared. Twenty cutinase orthologues were detected among different fungal species, whose common ancestor is Pezizomycotina and it is purported that these orthologues arose through a single gene duplication event prior to speciation. The cutinase domain was retained both in structure and arrangement among 34 different Colletotrichum species. The order of aligned genomic blocks between species and the arrangement of flanking protein domains were also conserved and shared for those domains immediately located at the N‐ and C‐terminus of the cutinase domain. Among these were an RNA recognition motif, translation elongation factor, signal peptide, pentatricopeptide repeat, and Hsp70 family of chaperone proteins, all of which support the expression of the cutinase gene. The findings of this study are important to understanding the evolution of the cutinase gene in C. truncatum as a key component of the biotrophic–necrotrophic switch which may be useful in developing gene‐targeting strategies to decrease the pathogenic potential of Colletotrichum species.

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OMA standalone: orthology inference among public and custom genomes and transcriptomes

Abstract: The correction has been made in the revised article online.

Cited by 135 publications

References 95 publications

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

Undinarchaeota illuminate the evolution of DPANN archaea

Diversity, structure, and synteny of the cutinase gene ofColletotrichumspecies

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