Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats.

Autor: Palacios-Gimenez OM; Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. octavio.palacios@ebc.uu.se.; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. octavio.palacios@ebc.uu.se., Koelman J; Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden., Palmada-Flores M; Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden., Bradford TM; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia.; School of Biological Sciences and Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, 5005, Australia., Jones KK; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia., Cooper SJB; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia.; School of Biological Sciences and Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, 5005, Australia., Kawakami T; Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. tkawakami@embarkvet.com.; Embark Veterinary, Inc., Boston, MA, USA. tkawakami@embarkvet.com., Suh A; Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. alexander.suh@ebc.uu.se.; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. alexander.suh@ebc.uu.se.; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK. alexander.suh@ebc.uu.se.
Jazyk: angličtina
Zdroj: BMC biology [BMC Biol] 2020 Dec 21; Vol. 18 (1), pp. 199. Date of Electronic Publication: 2020 Dec 21.
DOI: 10.1186/s12915-020-00925-x
Abstrakt: Background: Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the "repeatome", are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution.
Results: We obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex.
Conclusion: This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.
Databáze: MEDLINE
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