Species sympatry and horizontal transfers of Mariner transposons in marine crustacean genomes

Casse, Nathalie; Bui, Quynh-Trang; Nicolas, Violaine; Renault, Sylvie; Bigot, Yves; Laulier, M.

doi:10.1016/j.ympev.2006.02.005

Cited by 35 publications

(43 citation statements)

References 31 publications

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“…In addition, it appears that GalEa1 elements are highly conserved at the DNA level in geographically widespread species. Such pattern is similar to the distribution and copy conservation observed for the Sea Urchin Retroviral-Like (SURL) elements (Gonzalez and Lessios 1999) or mariner-like elements in marine crustacean genomes (Casse et al 2006). Moreover, the high conservation level of GalEa1 between Galatheidae and Chirostylidae raises the question of its distribution among Galatheidea or, more largely, among Anomoura.…”

Section: Discussionsupporting

confidence: 70%

“…To date, only a few TEs have been described in crustacean species: retroposon R2 in an isopod and in horseshoe crab , transposon Pokey from the piggyBac superfamily in a waterXea (Penton et al 2002) and marinerlike transposons (Casse et al 2000(Casse et al , 2006Kvamme et al 2005;Bui et al 2007), jockey-like and CR1-like retroposons (Halaimia-Toumi et al 2004) in hydrothermal and coastal crabs. No LTR retrotransposon has been described to date.…”

Section: Introductionmentioning

confidence: 99%

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GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species

2007

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Crustacean species have not been examined in great detail for their transposable elements content. Here we focus on galatheid crabs, which are one of the most diverse and widespread taxonomic groups of Decapoda. Ty1/copia retrotransposons are a diverse and taxonomically dispersed group. Using degenerate primers, we isolated several DNA fragments that show homology with Ty1/copia retroelements reverse transcriptase gene. We named the corresponding elements from which they originated GalEa1 to GalEa3 and analyzed one of them further by isolating various clones containing segments of GalEa1. This is the first LTR retrotransposon described in crustacean genome. Nucleotide sequencing of the clones revealed that GalEa1 has LTRs (124 bp) and that the internal sequence (4,421 bp) includes a single large ORF containing gag and pol regions. Further screening identified highly related elements in six of the nine galatheid species studied. By performing BLAST searches on genome databases, we could also identify GalEa-like elements in some fishes and Urochordata genomes. These elements define a new clade of Ty1/copia retrotransposons that differs from all other Ty1/copia elements and that seems to be restricted to aquatic species.

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Section: Discussionsupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species

2007

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“…This hypothesis has previously been suggested as the mechanism of genome size variation in various plant species (e.g., Rayburn and Auger 1990;Bennetzen et al 2005) but has not been studied in depth within animals or crustaceans specifically. Transposable elements have been characterized from different crustacean lineages (e.g., Casse et al 2006;Vergilino et al 2013), though their direct contributions to differences in genome size have not yet been quantified.…”

Section: Discussionmentioning

confidence: 99%

Patterns of genome size variation in snapping shrimp

Jeffery

Hultgren

Chak

et al. 2016

Genome

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Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.Key words: Synalpheus, genome size, C-value, polyploidy, gene duplication, chromosome. Résumé :Bien que les crustacés présentent une variation considérable en matière de taille de leurs génomes, peu de choses sont connues sur les liens entre la taille du génome et l'écologie ainsi que l'évolution des espèces au sein de ce large groupe. Cela découle en partie de l'absence de grands jeux de données. Dans ce travail, les auteurs ont étudié la variation pour la taille du génome aux niveaux interspécifique, intraspécifique et intracolonie chez 39 espèces de crevettes du genre Synalpheus, constituant ainsi l'un des plus grands jeux de données sur la taille des génomes au sein d'un seul genre parmi les crustacés. Les auteurs trouvent que la taille du génome va du simple au quadruple chez les Synalpheus, sans pour autant générer un signal phylogénétique ou qu'il y ait de lien avec la taille de l'organisme. Au sein de ce sous-ensemble d'espèces, la taille du génome est corrélée avec la taille des chromosomes mais pas leur nombre, ce qui suggère que les grands génomes ne sont pas le résultat de la polyploïdie de ces espèces. Ce qui est intéressant, c'est qu'il semble y avoir une variation intraspécifique pour la taille du génome de 35 % chez l'espèce Synalpheus idios, en fonction de l'origine géographique des spécimens, et jusqu'à 30 % au sein de spécimens du Synalpheus duffyi provenant de la même colonie. [Traduit par la Rédaction]

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“…This 1,286-bp element, initially designated pch, includes a single open reading frame encoding a protein of 345 amino acids with TIRs of 28 bp at each extremity (Jacobson et al 1986). Since then, numerous mariner elements have been characterized in nematodes (Leroy et al 2003), crustaceans (Casse et al 2006;Bui et al 2007Bui et al , 2008, fish (Ivics et al 1997), human beings (Augé-Gouillou et al 1995;Robertson and Zumpano 1997;Robertson and Martos 1997), plants (Casacuberta et al 1998;Feschotte and Wessler 2002;Zhou et al 2010), protozoans (Silva et al 2005), and insects (Robertson 1993;Robertson and McLeod 1993;Rouleux-Bonnin et al 2005;Wang et al 2011;Rezende-Teixeira et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Characterization of mariner-like transposons of the mauritiana Subfamily in seven tree aphid species

et al. 2015

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Mariner-like elements (MLEs) are Class II transposons present in all eukaryotic genomes in which MLEs have been searched for. This article reports the detection of MLEs in seven of the main fruit tree aphid species out of eight species studied. Deleted MLE sequences of 916-919 bp were characterized, using the terminal-inverted repeats (TIRs) of mariner elements belonging to the mauritiana Subfamily as primers. All the sequences detected were deleted copies of full-length elements that included the 3'- and 5'-TIRs but displayed internal deletions affecting Mos1 activity. Networks based on the mtDNA cytochrome oxidase subunit-I (CO-I) and MLE sequences were incongruent, suggesting that mutations in transposon sequences had accumulated before speciation of tree aphid species occurred, and that they have been maintained in this species via vertical transmissions. This is the first evidence of the widespread occurrence of MLEs in aphids.

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Species sympatry and horizontal transfers of Mariner transposons in marine crustacean genomes

Cited by 35 publications

References 31 publications

GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species

GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species

Patterns of genome size variation in snapping shrimp

Characterization of mariner-like transposons of the mauritiana Subfamily in seven tree aphid species

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