The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA

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.

Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

“…The detection of 52 satDNAs constituting the satellitome of the Pacific oyster (Table 1) is a giant leap in the knowledge about the satDNA content of this species, up until now limited to only three satDNAs (reviewed in [34]). The employment of NGS methods has immensely improved satDNA detection substantially increasing the number of satDNAs detected in the genomes of many species (e.g., [9][10][11]52,53]). Although satDNA monomer lengths vary significantly in the satellitome of the Pacific oyster, 160-180 bp-long monomers predominate.…”

Comparative transcriptome analysis of noble crayfish and marbled crayfish immune response to Aphanomyces astaci challenges

“…Consequently, generating first high-quality genome assemblies for freshwater crayfish represents a priority in the field of crayfish immunity, and would allow for the future comprehensive epigenomic studies. Unfortunately, until now this has proven to be a challenging task, because freshwater crayfish genomes are often large in size and have a high proportion of repetitive DNA sequences [31,146,147]. Furthermore, while in Decapods the role of the hepatopancreas in the immune response against pathogens has already been demonstrated, it has to be considered that the observed expression profile might be influenced by the infiltrating haemocytes [16,104].…”

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

“…We have applied short read sequencing followed by read clustering to efficiently gain insights into both genomes’ satDNA contents (as laid out by Weiss-Schneeweiss et al, 2015 ; Novák et al, 2017 ). This approach has been successfully used to characterize the repeat landscapes of many non-model plant species as for example beans, various grasses, camellias, crocuses, quinoa, and ferns ( Cai et al, 2014 ; Heitkam et al, 2015 ; Ávila Robledillo et al, 2018 ; Kirov et al, 2018 ; Liu et al, 2019 ; Schmidt et al, 2019 ; Heitkam et al, 2020 ; Ribeiro et al, 2020 ), and also of non-model animals, such as locusts, grasshoppers, or fishes ( Ruiz-Ruano et al, 2016 ; Ferretti et al, 2020 ; Boštjančić et al, 2021 ). For larch genomes, we provided evidence that LTR retrotransposons and derived fragments are their main components, well in line with reports for the related pines and spruces ( Kamm et al, 1996 ; Kossack and Kinlaw, 1999 ; Nystedt et al, 2013 ; Stevens et al, 2016 ; Voronova et al, 2017 ; Perera et al, 2018 ).…”