Abstract
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.
Highlights
Freshwater crayfish constitute a monophyletic group of over 640 described species, arranged into four families: Astacidae, Cambaridae, Cambaroididae, and Parastacidae (Crandall and De Grave, 2017)
Keeping in mind the lack of research in the field for European freshwater crayfish, this study aims to: (i) identify and characterize repetitive sequences in the P. leptodactylus genome in order to get better insight into genome organization and evolution of this species, and (ii) analyze the chromosomal distribution patterns of major tandem repetitive DNA families to contribute with the chromosome organization and evolution
Phylogenetic tree was constructed to place samples used in this study within the context of patterns of diversity across the range of P. leptodactylus
Summary
Freshwater crayfish constitute a monophyletic group of over 640 described species, arranged into four families: Astacidae, Cambaridae, Cambaroididae, and Parastacidae (Crandall and De Grave, 2017). These species are distributed across all but the Antarctic continent, the Indian subcontinent, and African mainland, with centers of diversity in the southeastern Appalachian Mountains in the North America and southeastern Australia (Crandall and Buhay, 2008). One of the native European crayfish species is Pontastacus leptodactylus (Eschscholtz, 1823), found both in freshwater and brackish environments with a nowadays distribution encompassing Europe, eastern Russia, and the Middle East (Kouba et al, 2014). While genomic information has started to accumulate for North American and Australian species (Gutekunst et al, 2018; Tan et al, 2020; Van Quyen et al, 2020), so far few studies have focused on cytogenetic and genome organization of European freshwater crayfish species (Mlinarec et al, 2011, 2016), and the general aim of this study was to increase knowledge on genome evolution and diversity focusing on repetitive DNAs in P. leptodactylus
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