The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA
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...
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doaj-55d0fba2908a444f9d9ba12aa4f9104a2021-01-21T09:53:45ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.611745611745The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNALjudevit Luka Boštjančić0Lena Bonassin1Lucija Anušić2Leona Lovrenčić3Višnja Besendorfer4Ivana Maguire5Frederic Grandjean6Christopher M. Austin7Carola Greve8Alexander Ben Hamadou9Jelena Mlinarec10Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CroatiaDivision of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CroatiaDivision of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CroatiaDivision of Zoology, Department of Biology, University of Zagreb, Zagreb, CroatiaDivision of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CroatiaDivision of Zoology, Department of Biology, University of Zagreb, Zagreb, CroatiaLaboratoire Ecologie Biologie des Interactions-UMR CNRS 7267, University of Poitiers, Poitiers, FranceCentre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, AustraliaLOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, GermanyLOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, GermanyDivision of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CroatiaPontastacus 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.https://www.frontiersin.org/articles/10.3389/fgene.2020.611745/fullFISHgenome sizeinterstitial telomeric repeatskaryotypenarrow-clawed crayfish(peri)centromeric heterochromatin |
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language |
English |
format |
Article |
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DOAJ |
author |
Ljudevit Luka Boštjančić Lena Bonassin Lucija Anušić Leona Lovrenčić Višnja Besendorfer Ivana Maguire Frederic Grandjean Christopher M. Austin Carola Greve Alexander Ben Hamadou Jelena Mlinarec |
spellingShingle |
Ljudevit Luka Boštjančić Lena Bonassin Lucija Anušić Leona Lovrenčić Višnja Besendorfer Ivana Maguire Frederic Grandjean Christopher M. Austin Carola Greve Alexander Ben Hamadou Jelena Mlinarec The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA Frontiers in Genetics FISH genome size interstitial telomeric repeats karyotype narrow-clawed crayfish (peri)centromeric heterochromatin |
author_facet |
Ljudevit Luka Boštjančić Lena Bonassin Lucija Anušić Leona Lovrenčić Višnja Besendorfer Ivana Maguire Frederic Grandjean Christopher M. Austin Carola Greve Alexander Ben Hamadou Jelena Mlinarec |
author_sort |
Ljudevit Luka Boštjančić |
title |
The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA |
title_short |
The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA |
title_full |
The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA |
title_fullStr |
The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA |
title_full_unstemmed |
The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA |
title_sort |
pontastacus leptodactylus (astacidae) repeatome provides insight into genome evolution and reveals remarkable diversity of satellite dna |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-01-01 |
description |
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. |
topic |
FISH genome size interstitial telomeric repeats karyotype narrow-clawed crayfish (peri)centromeric heterochromatin |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2020.611745/full |
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