scholarly journals Genome streamlining in a minute herbivore that manipulates its host plant

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Robert Greenhalgh ◽  
Wannes Dermauw ◽  
Joris J Glas ◽  
Stephane Rombauts ◽  
Nicky Wybouw ◽  
...  
Keyword(s):  
Gene Families ◽  
Natural Resistance ◽  
Environmental Response ◽  
Ecological Specialization ◽  
Response Gene ◽  
Genomic Features ◽  
Evolutionary Forces ◽  
Microbial Eukaryotes ◽  
Intergenic Regions ◽  
Tomato Russet Mite

The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host’s natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite’s minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species’ highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.

scholarly journals Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

2021 ◽  
Author(s):  
Kim Vertacnik ◽  
Danielle Herrig ◽  
R Keating Godfrey ◽  
Tom Hill ◽  
Scott Geib ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Size ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Gene Gain ◽  
Ecological Specialization ◽  
Dietary Specialization ◽  
Pine Sawfly ◽  
Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

scholarly journals Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Raúl A. González-Pech ◽  
Timothy G. Stephens ◽  
Yibi Chen ◽  
Amin R. Mohamed ◽  
Yuanyuan Cheng ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Families ◽  
Specific Gene ◽  
Free Living ◽  
Microbial Eukaryotes ◽  
The Family ◽  
Structural Divergence ◽  
Genome Features ◽  
Genome Divergence ◽  
Genome Assemblies

Abstract Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features. Results Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. Conclusions Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.

scholarly journals Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia

2019 ◽  
Vol 11 (10) ◽  
pp. 2887-2894 ◽  
Author(s):  
Carolina Alejandra Martinez-Gutierrez ◽  
Frank O Aylward
Keyword(s):  
Genome Size ◽  
Purifying Selection ◽  
Marker Genes ◽  
Marine Microorganisms ◽  
Phylogenetic Groups ◽  
Genomic Features ◽  
Region Length ◽  
Intergenic Regions ◽  
Global Biogeochemical Cycles ◽  
Low Nitrogen

Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G + C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here, we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of nonsynonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared with their mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G + C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that microbes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.

scholarly journals Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sarah Farhat ◽  
Phuong Le ◽  
Ehsan Kayal ◽  
Benjamin Noel ◽  
Estelle Bigeard ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Protein Evolution ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Gene Families ◽  
Gene Organization ◽  
Host Specialization ◽  
Evolutionary Mechanisms ◽  
Symbiotic Relationships ◽  
Intergenic Regions

Abstract Background Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. Results We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. Conclusion These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.

scholarly journals Protist.Guru: A Comparative Transcriptomics Database for the Protist Kingdom

2021 ◽  
Author(s):  
Erielle Marie Fajardo Villanueva ◽  
Peng Ken Lim ◽  
Jolyn Jia Jia Lim ◽  
ShanChun Lim ◽  
Pei Yi Lau ◽  
...  
Keyword(s):  
Gene Families ◽  
Gene Clusters ◽  
Biological Processes ◽  
Expression Data ◽  
Online Database ◽  
Microbial World ◽  
Microbial Eukaryotes ◽  
Haematococcus Lacustris ◽  
Secondary Carotenoids ◽  
Protist Species

Abstract Summary: During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still neglected. To address this gap, we used gene expression data from 15 distinct protist species to create protist.guru: an online database equipped with tools for identifying functional co-expression networks, gene families, and enriched gene clusters. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. Availability: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.

scholarly journals Genomic and Morphological Features of a Banchine Polydnavirus: Comparison with Bracoviruses and Ichnoviruses

2007 ◽  
Vol 81 (12) ◽  
pp. 6491-6501 ◽  
Author(s):  
Renée Lapointe ◽  
Kohjiro Tanaka ◽  
Walter E. Barney ◽  
James B. Whitfield ◽  
Jonathan C. Banks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Size ◽  
Genome Sequence ◽  
Protein Tyrosine Phosphatase ◽  
Size Range ◽  
Tyrosine Phosphatase ◽  
Gene Families ◽  
Open Reading Frames ◽  
Genomic Features ◽  
Reading Frames

ABSTRACT Many ichneumonid and braconid endoparasitoids inject a polydnavirus (PDV) into their caterpillar hosts during oviposition. The viral entities carried by wasps of these families are referred to as “ichnoviruses” (IVs) and “bracoviruses” (BVs), respectively. All IV genomes characterized to date are found in wasps of the subfamily Campopleginae; consequently, little is known about PDVs found in wasps of the subfamily Banchinae, the only other ichneumonid taxon thus far shown to carry these viruses. Here we report on the genome sequence and virion morphology of a PDV carried by the banchine parasitoid Glypta fumiferanae. With an aggregate genome size of ∼290 kb and 105 genome segments, this virus displays a degree of genome segmentation far greater than that reported for BVs or IVs. The size range of its genome segments is also lower than those in the latter two groups. As reported for other PDVs, the predicted open reading frames of this virus cluster into gene families, including the protein tyrosine phosphatase (PTP) and viral ankyrin (ank) families, but phylogenetic analysis indicates that ank genes of the G. fumiferanae virus are not embedded within the IV lineage, while its PTPs and those of BVs form distinct clusters. The banchine PDV genome also encodes a novel family of NTPase-like proteins displaying a pox-D5 domain. The unique genomic features of the first banchine virus examined, along with the morphological singularities of its virions (IV-like nucleocapsids, but enveloped in groups like some of the BVs), suggest that they could have an origin distinct from those of IVs and BVs.

Resistance genes against plant-parasitic nematodes: a durable control strategy?

Nematology ◽  
2015 ◽  
Vol 17 (3) ◽  
pp. 249-263 ◽  
Author(s):  
Laura J. Davies ◽  
Axel A. Elling
Keyword(s):  
Natural Resistance ◽  
Economic Losses ◽  
Parasitic Nematodes ◽  
Agricultural Systems ◽  
Plant Parasitic Nematodes ◽  
Cyst Nematodes ◽  
Evolutionary Forces ◽  
Plant Nematode ◽  
Major Pest ◽  
Plant Parasitic

Plant-parasitic nematodes are a major pest of all agricultural systems, causing extensive economic losses. Natural resistance (R) genes offer an alternative to chemical control and have been shown effectively to limit nematode damage to crops in the field. Whilst a number of resistant cultivars have conferred resistance against root-knot and cyst nematodes for many decades, an increasing number of reports of resistance-breaking nematode pathotypes are beginning to emerge. The forces affecting the emergence of virulent nematodes are complex, multifactorial and involve both the host and parasite of the plant-nematode interaction. This review provides an overview of the root-knot and cyst nematodeRgenes characterised to date, in addition to examining the evolutionary forces influencing nematode populations and the emergence of virulence. Finally, potential strategies to improveRgene durability in the field are outlined, and areas that would benefit from further research efforts are highlighted.

scholarly journals Pathogenomics of EmergingCampylobacterSpecies

2019 ◽  
Vol 32 (4) ◽  
Author(s):  
Daniela Costa ◽  
Gregorio Iraola
Keyword(s):  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Genomic Features ◽  
Content Type ◽  
Evolutionary Forces ◽  
Clinical Awareness ◽  
Future Work

SUMMARYCampylobacteris among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reportedCampylobacterinfections are caused byCampylobacter jejuniand, to a lesser extent,C. coli; however, the increasing recognition of other emergingCampylobacterpathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such asC. fetusandC. concisus. These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emergingCampylobacterspecies, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.

scholarly journals Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Abigail L. Lind ◽  
Katherine S. Pollard
Keyword(s):  
Gene Families ◽  
Shotgun Sequencing ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Dna And Rna ◽  
Paired Samples ◽  
Microbial Eukaryotes ◽  
Conserved Gene

Abstract Background Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded. Results Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. Conclusions EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes.

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