Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis

Luchetti, Andrea; Forni, Giobbe; Martelossi, Jacopo; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Skaist, Alyza; Wheelan, Sarah J.; Mantovani, Barbara

doi:10.1016/j.ygeno.2021.11.001

Cited by 8 publications

(5 citation statements)

References 85 publications

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“…Most importantly, triops exhibit very active swimming, with naturally different behavioural types and types specifically elicited by distinct toxicants, which is useful for profiling. Lastly, they are also amenable to complementary molecular investigations that can bring knowledge on the modes of action of chemicals on exposed animals [40,44,45]. In particular, compared with the well-established freshwater model Daphnia magna, triops are about ten times bigger, which facilitates carrying out analyses in individuals, such as the determination of biochemical and other molecular biomarkers.…”

Section: Resultsmentioning

confidence: 99%

Sensitivity of Triops longicaudatus Locomotor Behaviour to Detect Short Low-Level Exposure to Pollutants

Guimarães,

Carvalho,

Ribeiro

et al. 2023

Water

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Triops longicaudatus is a crustacean typically inhabiting temporary freshwater bodies in regions with a Mediterranean climate. These crustaceans are easily maintained in the laboratory and show a set of biological features that make them good candidates for diagnosing environmental quality and health. However, information about their responses to environmental contamination is scarce. This study characterised the locomotor responses of juvenile and adult/mature T. longicaudatus to low concentrations of five model toxicants upon a very short 1.5 h exposure: tributyltin, mercury, lindane, sodium hypochlorite and formaldehyde. A video-tracking system was used to record the locomotor behaviour. The data were analysed with an artificial neural network to identify distinct behaviours, followed by Chi-square and Correspondence analysis to characterise the response to each toxicant. The results showed that T. longicaudatus is sensitive to aquatic contamination, particularly sodium hypochlorite. Six behaviour types were defined, which allowed for the characterisation and discrimination of the test toxicants. The results support the need for more investigation into this species and its behaviour types as an alternative to animal testing and the more apical and often invasive endpoints commonly recommended in standard guidelines.

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Section: Resultsmentioning

confidence: 99%

Sensitivity of Triops longicaudatus Locomotor Behaviour to Detect Short Low-Level Exposure to Pollutants

Guimarães,

Carvalho,

Ribeiro

et al. 2023

Water

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“…We obtained new mitogenomes from ongoing genome projects of four species 35 : Lepidurus couesii Packard, 1875, Lepidurus apus apus (Linnaeus, 1758), Triops longicaudatus (LeConte, 1846) and Leptestheria dahalacensis (Rüppel, 1837). The length of mitogenomes ranges from 15,105 bp ( L. dahalacensis ) to 15,292 bp ( L. couesii ), and they all show 13 PCGs, 22 tRNAs and two rRNAs genes.…”

Section: Resultsmentioning

confidence: 99%

“…Since the first study of GO rearrangements in Branchiopoda, though, new mitogenomes have become available in public databases for several lineages, in particular for Cladocera. Along with the previously analyzed dataset, we further considered five new mitogenomes, de novo assembled from genome sequencing data 34 , 35 , and 37 mitogenomes which become available from NCBI GenBank (39 sequences from recently published papers listed in Suppl. Table S1 and three from the DNAmark Project [ https://dnamark.ku.dk/ ]).…”

Section: Introductionmentioning

confidence: 99%

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

Castellucci

Luchetti

Mantovani

2022

Sci Rep

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The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.

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“…TEs comprise a large proportion of the genome in eukaryotes, but signi cant differences in TE content are commonly observed in both vertebrate and invertebrate lineages and even in closely phylogenetic taxas (Luchetti et al 2021). In the genomes of 24 mosquitoes, TEs accounted for the lowest proportion at 0.13% of the genome in Anopheles farauti and the highest proportion exceeding 50% in Aedes aegypti.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution

Xu,

Tang,

Feng

et al. 2023

Mar Biotechnol

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Transposable elements (TEs) are mobile genetic elements that exist in the host genome and exert considerable in uence on the evolution of the host genome. Since crustaceans, including decapoda, are considered ideal models for studying the relationship between adaptive evolution and TEs, TEs were identi ed and classi ed in the genomes of eight decapoda species and one diplostraca species (as the outgroup) using two strategies, namely homology-based annotation and de novo annotation. The statistics and classi cation of TEs showed that their proportion in the genome and their taxonomic composition in decapoda were different. Moreover, correlation analysis and transcriptome data demonstrated that there were more PIF-Harbinger TEs in the genomes of Eriocheir sinensis and Scylla paramamosain, and the expression patterns of PIF-Harbingers were signi cantly altered under air exposure stress conditions. These results signaled that PIF-Harbingers expanded in the genome of E. sinensis and S. paramamosain and might be related to their air exposure tolerance levels. Meanwhile, sequence alignment revealed that some Jockey-like sequences (JLSs) with high similarity to speci c regions of the White spot syndrome virus (WSSV) genome existed in all eight decapod species. At the same time, phylogenetic comparison exposed that the phylogenetic tree constructed by JLSs was not in agreement with that of the species tree, and the distribution of each branch was signi cantly different. The above-mentioned results signaled that these WSSV-speci c JLSs might originate from the endogenesis of WSSV and were horizontally transferred via WSSV. This study accumulated data for expanding research on TEs in decapod species and also provided new insights and future direction for the breeding of stress-resistant and disease-resistant crab breeds.

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Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis

Cited by 8 publications

References 85 publications

Sensitivity of Triops longicaudatus Locomotor Behaviour to Detect Short Low-Level Exposure to Pollutants

Sensitivity of Triops longicaudatus Locomotor Behaviour to Detect Short Low-Level Exposure to Pollutants

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution

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