Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies
Fish chromosomes are considered homogeneous in their AT/GC nucleotide composition, and banding patterns enabling identification of homologs are largely missing. While cytogenomic approaches try to compensate for this issue by virtual karyotyping, they rely on the quality of genome assemblies availab...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Fishes |
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| Online Access: | https://www.mdpi.com/2410-3888/8/4/185 |
| _version_ | 1797605523322830848 |
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| author | Marta Vohnoutová Lucia Žifčáková Radka Symonová |
| author_facet | Marta Vohnoutová Lucia Žifčáková Radka Symonová |
| author_sort | Marta Vohnoutová |
| collection | DOAJ |
| description | Fish chromosomes are considered homogeneous in their AT/GC nucleotide composition, and banding patterns enabling identification of homologs are largely missing. While cytogenomic approaches try to compensate for this issue by virtual karyotyping, they rely on the quality of genome assemblies available. Recently, soft-masked genome assemblies combining costly and arduous long- and short-read sequencing and new generation assemblers became available for two teleost fish species, climbing perch (<i>Anabas testudineus</i>) and channel bull blenny (<i>Cottoperca gobio</i>). Soft-masking turns repetitive sequences in a genome assembly into lower case letters, leaving unique sequences in upper case. This enables investigators to assess the proportion of guanine and cytosine nucleotides (GC%) of transposable elements as an indicator of AT/GC homogenisation in fish. We have developed a new version of our Python tool Evan, which utilises chromosome-level genome assemblies and combines the profiles of GC% and the proportion of repeats (rep%) along chromosomes. Our profiles of both of those fishes showed clear and abrupt but small-scale fluctuations in GC% along otherwise compositionally homogenised sequences. Our study also highlights the key role of the sliding window size in determining the resolution of GC% profiling. While the quality of the genome assemblies appeared to be sufficient for GC%/rep% profiling, more effective repeat masking is necessary to better distinguish to what extent repeats compositionally homogenize fish genomes. |
| first_indexed | 2024-03-11T05:02:18Z |
| format | Article |
| id | doaj.art-9e4c38645f794509bbab919fae977d27 |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-11T05:02:18Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Fishes |
| spelling | doaj.art-9e4c38645f794509bbab919fae977d272023-11-17T19:12:26ZengMDPI AGFishes2410-38882023-03-018418510.3390/fishes8040185Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome AssembliesMarta Vohnoutová0Lucia Žifčáková1Radka Symonová2Department of Computer Science, Faculty of Science, University of South Bohemia in České Budějovice, 370-05 České Budějovice, Czech RepublicOkinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, JapanDepartment of Computer Science, Faculty of Science, University of South Bohemia in České Budějovice, 370-05 České Budějovice, Czech RepublicFish chromosomes are considered homogeneous in their AT/GC nucleotide composition, and banding patterns enabling identification of homologs are largely missing. While cytogenomic approaches try to compensate for this issue by virtual karyotyping, they rely on the quality of genome assemblies available. Recently, soft-masked genome assemblies combining costly and arduous long- and short-read sequencing and new generation assemblers became available for two teleost fish species, climbing perch (<i>Anabas testudineus</i>) and channel bull blenny (<i>Cottoperca gobio</i>). Soft-masking turns repetitive sequences in a genome assembly into lower case letters, leaving unique sequences in upper case. This enables investigators to assess the proportion of guanine and cytosine nucleotides (GC%) of transposable elements as an indicator of AT/GC homogenisation in fish. We have developed a new version of our Python tool Evan, which utilises chromosome-level genome assemblies and combines the profiles of GC% and the proportion of repeats (rep%) along chromosomes. Our profiles of both of those fishes showed clear and abrupt but small-scale fluctuations in GC% along otherwise compositionally homogenised sequences. Our study also highlights the key role of the sliding window size in determining the resolution of GC% profiling. While the quality of the genome assemblies appeared to be sufficient for GC%/rep% profiling, more effective repeat masking is necessary to better distinguish to what extent repeats compositionally homogenize fish genomes.https://www.mdpi.com/2410-3888/8/4/185chromosome visualisationvirtual karyotypingGC contentrepetitive sequences |
| spellingShingle | Marta Vohnoutová Lucia Žifčáková Radka Symonová Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies Fishes chromosome visualisation virtual karyotyping GC content repetitive sequences |
| title | Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies |
| title_full | Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies |
| title_fullStr | Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies |
| title_full_unstemmed | Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies |
| title_short | Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies |
| title_sort | hidden compositional heterogeneity of fish chromosomes in the era of polished genome assemblies |
| topic | chromosome visualisation virtual karyotyping GC content repetitive sequences |
| url | https://www.mdpi.com/2410-3888/8/4/185 |
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