Insights into the genomic evolution of insects from cricket genomes.
Ontology highlight
ABSTRACT:
SUBMITTER: Ylla G
PROVIDER: S-EPMC8203789 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Phylogenetic relationships of basal insects remain a matter of discussion. In particular, the relationships among Ephemeroptera, Odonata and Neoptera are the focus of debate. In this study, we used a next-generation sequencing approach to reconstruct new mitochondrial genomes (mitogenomes) from 18 species of basal insects, including six representatives of Ephemeroptera and 11 of Odonata, plus one species belonging to Zygentoma. We then compared the structures of the newly sequenced mitogenomes. A tRNA gene cluster of IMQM was found in three ephemeropteran species, which may serve as a potential synapomorphy for the family Heptageniidae. Combined with published insect mitogenome sequences, we constructed a data matrix with all 37 mitochondrial genes of 85 taxa, which had a sampling concentrating on the palaeopteran lineages. Phylogenetic analyses were performed based on various data coding schemes, using maximum likelihood and Bayesian inferences under different models of sequence evolution. Our results generally recovered Zygentoma as a monophyletic group, which formed a sister group to Pterygota. This confirmed the relatively primitive position of Zygentoma to Ephemeroptera, Odonata and Neoptera. Analyses using site-heterogeneous CAT-GTR model strongly supported the Palaeoptera clade, with the monophyletic Ephemeroptera being sister to the monophyletic Odonata. In addition, a sister group relationship between Palaeoptera and Neoptera was supported by the current mitogenomic data.
| S-EPMC6883079 | biostudies-literature
Project description:BACKGROUND:As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution. RESULTS:We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page CONCLUSION:Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic resources for three distinct but overlapping fields of inquiry: neurobiology, speciation, and molecular evolution.
| S-EPMC1878485 | biostudies-literature
Project description:Genomes evolve through a combination of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. This leads to differences in branch-length patterns among gene trees. Genes that yield trees with the same branch-length patterns can be grouped together into clusters. Here, we propose a novel phylogenetic approach to explain the factors that influence the number and distribution of these gene-tree clusters. We apply our method to a genomic dataset from insects, an ancient and diverse group of organisms. We find some evidence that when drift is the dominant evolutionary process, each cluster tends to contain a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct clusters, each of which contains only a few slow-evolving genes. Our work, although preliminary in nature, illustrates the use of phylogenetic methods to shed light on the factors driving rate variation in genomic evolution.
| S-EPMC5410144 | biostudies-literature
Project description:Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.
| S-EPMC4085046 | biostudies-literature
Project description:The unique nomadic life-history pattern of army ants (army ant adaptive syndrome), including obligate colony fission and strongly male-biased sex-ratios, makes army ants prone to heavily reduced effective population sizes (Ne). Excessive multiple mating by queens (polyandry) has been suggested to compensate these negative effects by increasing genetic variance in colonies and populations. However, the combined effects and evolutionary consequences of polyandry and army ant life history on genetic colony and population structure have only been studied in a few selected species. Here we provide new genetic data on paternity frequencies, colony structure and paternity skew for the five Neotropical army ants Eciton mexicanum, E. vagans, Labidus coecus, L. praedator and Nomamyrmex esenbeckii; and compare those data among a total of nine army ant species (including literature data). The number of effective matings per queen ranged from about 6 up to 25 in our tested species, and we show that such extreme polyandry is in two ways highly adaptive. First, given the detected low intracolonial relatedness and population differentiation extreme polyandry may counteract inbreeding and low Ne. Second, as indicated by a negative correlation of paternity frequency and paternity skew, queens maximize intracolonial genotypic variance by increasingly equalizing paternity shares with higher numbers of sires. Thus, extreme polyandry is not only an integral part of the army ant syndrome, but generally adaptive in social insects by improving genetic variance, even at the high end spectrum of mating frequencies.
| S-EPMC4140799 | biostudies-literature
Project description:BACKGROUND:Opsins are key proteins in animal photoreception. Together with a light-sensitive group, the chromophore, they form visual pigments which initiate the visual transduction cascade when photoactivated. The spectral absorption properties of visual pigments are mainly determined by their opsins, and thus opsins are crucial for understanding the adaptations of animal eyes. Studies on the phylogeny and expression pattern of opsins have received considerable attention, but our knowledge about insect visual opsins is still limited. Up to now, researchers have focused on holometabolous insects, while general conclusions require sampling from a broader range of taxa. We have therefore investigated visual opsins in the ocelli and compound eyes of the two-spotted cricket Gryllus bimaculatus, a hemimetabolous insect. RESULTS:Phylogenetic analyses place all identified cricket sequences within the three main visual opsin clades of insects. We assign three of these opsins to visual pigments found in the compound eyes with peak absorbances in the green (515 nm), blue (445 nm) and UV (332 nm) spectral range. Their expression pattern divides the retina into distinct regions: (1) the polarization-sensitive dorsal rim area with blue- and UV-opsin, (2) a newly-discovered ventral band of ommatidia with blue- and green-opsin and (3) the remainder of the compound eye with UV- and green-opsin. In addition, we provide evidence for two ocellar photopigments with peak absorbances in the green (511 nm) and UV (350 nm) spectral range, and with opsins that differ from those expressed in the compound eyes. CONCLUSIONS:Our data show that cricket eyes are spectrally more specialized than has previously been assumed, suggesting that similar adaptations in other insect species might have been overlooked. The arrangement of spectral receptor types within some ommatidia of the cricket compound eyes differs from the generally accepted pattern found in holometabolous insect taxa and awaits a functional explanation. From the opsin phylogeny, we conclude that gene duplications, which permitted differential opsin expression in insect ocelli and compound eyes, occurred independently in several insect lineages and are recent compared to the origin of the eyes themselves.
| S-EPMC3502269 | biostudies-literature
Project description:BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, including muscle biology. Many miRNAs were described as exclusively or highly expressed in skeletal and/or cardiac muscle. However, knowledge on the genomic organization and evolution of muscle miRNAs has been unveiled in a reduced number of vertebrates and mostly only reflects their organization in mammals, whereas fish genomes remain largely uncharted. The main goal of this study was to elucidate particular features in the genomic organization and the putative evolutionary history of muscle miRNAs through a genome-wide comparative analysis of cartilaginous and bony fish genomes. RESULTS: As major outcomes we show that (1) miR-208 was unexpectedly absent in cartilaginous and ray-finned fish genomes whereas it still exist in other vertebrate groups; (2) miR-499 was intergenic in medaka and stickleback conversely to other vertebrates where this miRNA is intronic; (3) the zebrafish genome is the unique harboring two extra paralogous copies of miR-499 and their host gene (Myh7b); (4) a rare deletion event of the intergenic and bicistronic cluster miR-1-1/133a-2 took place only into Tetraodontiformes genomes (pufferfish and spotted green puffer); (5) the zebrafish genome experienced a duplication event of miR-206/-133b; and (6) miR-214 was specifically duplicated in species belonging to superorder Acanthopterygii. CONCLUSIONS: Despite of the aforementioned singularities in fish genomes, large syntenic blocks containing muscle-enriched miRNAs were found to persist, denoting colligated functionality between miRNAs and neighboring genes. Based on the genomic data here obtained, we envisioned a feasible scenario for explaining muscle miRNAs evolution in vertebrates.
| S-EPMC4177693 | biostudies-literature
Project description:Species in the genus Mucor have a worldwide distribution and are isolated from various substrata and hosts, including soil, dung, freshwater, and fruits. However, their diversity from insects is still much too little explored. The aim of this study was to characterize three new species of Mucor: Mucor grylli sp. nov., M. hyangburmii sp. nov., and M. kunryangriensis sp. nov., discovered in Kunryang-ri, Cheongyang in the Chungnam Province of Korea, during an investigation of Mucorales from cricket insects. The new species are described using morphological characters and molecular data including ITS and LSU rDNA regions. Mucor grylli is characterized by the highly variable shape of its columellae, which are subglobose to oblong, obovoid, strawberry-shaped, and sometimes slightly or strongly constricted in the center. Mucor hyangburmii is characterized by the production of azygospores and growth at 40 °C. Mucor kunryangriensis is characterized by the variable shape of its columellae, which are elongated-conical, obovoid, cylindrical ellipsoid, cylindrical, and production of abundant yeast-like cells on PDA, MEA, and SMA media. Based on the sequence analysis of two genetic markers, our phylogenic assessment strongly supported M. grylli, M. hyangburmii, and M. kunryangriensis as new species. Detailed descriptions, illustrations, and phylogenetic trees are provided.
| S-EPMC9224827 | biostudies-literature
Project description:This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10-13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ?360 million years ago.
| S-EPMC3238115 | biostudies-literature
Project description:Dipterocarpoideae, the largest subfamily of the Dipterocarpaceae, is a dominant component of Southeast Asian rainforests and is widely used as a source of wood, damar resin, medicine, and essential oil. However, many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human disturbance. Genetic information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes, providing clues to the function and evolution of these species. Here, we report on 13 high-quality Dipterocarpoideae genome assemblies, ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in Dipterocarpoideae. Molecular dating analyses support the Western Gondwanaland origin of Dipterocarpaceae. Based on evolutionary analysis, we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 chromosomes. We discovered an expansion of genes encoding cellulose synthase (CesA), which is essential for cellulose biosynthesis and secondary cell-wall formation. We functionally identified five bornyl diphosphate synthase (BPPS) genes, which specifically catalyze the biosynthesis of borneol, a natural medicinal compound extracted from damar resin and oils, thus providing a basis for large-scale production of natural borneol in vitro.
| S-EPMC9700207 | biostudies-literature