Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life

High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes – generically known as restriction-site associated DNA sequencing (RAD-seq) – is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design...

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Autores principales:	Herrera, Santiago, Reyes Herrera, Paula H., Shank, Timothy M.
Formato:	article
Lenguaje:	Inglés
Publicado:	Cold Sprimg Harbor Laboratory (CSH) 2025
Materias:	Investigación agropecuaria - A50 Árbol Genoma Enzima Diseño experimental Transversal http://aims.fao.org/aos/agrovoc/c_7887 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_2603 http://aims.fao.org/aos/agrovoc/c_29466
Acceso en línea:	https://www.biorxiv.org/content/10.1101/007781v2 http://hdl.handle.net/20.500.12324/40752

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institution	Corporación Colombiana de Investigación Agropecuaria
collection	Repositorio AGROSAVIA
language	Inglés
topic	Investigación agropecuaria - A50 Árbol Genoma Enzima Diseño experimental Transversal http://aims.fao.org/aos/agrovoc/c_7887 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_2603 http://aims.fao.org/aos/agrovoc/c_29466
spellingShingle	Investigación agropecuaria - A50 Árbol Genoma Enzima Diseño experimental Transversal http://aims.fao.org/aos/agrovoc/c_7887 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_2603 http://aims.fao.org/aos/agrovoc/c_29466 Herrera, Santiago Reyes Herrera, Paula H. Shank, Timothy M. Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
description	High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes – generically known as restriction-site associated DNA sequencing (RAD-seq) – is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is a knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for non-model species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition-sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting ‘neutral’ elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced-representation data is available (including transcriptomes and ‘neutral’ RAD-seq datasets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
format	article
author	Herrera, Santiago Reyes Herrera, Paula H. Shank, Timothy M.
author_facet	Herrera, Santiago Reyes Herrera, Paula H. Shank, Timothy M.
author_sort	Herrera, Santiago
title	Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
title_short	Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
title_full	Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
title_fullStr	Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
title_full_unstemmed	Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
title_sort	predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
publisher	Cold Sprimg Harbor Laboratory (CSH)
publishDate	2025
url	https://www.biorxiv.org/content/10.1101/007781v2 http://hdl.handle.net/20.500.12324/40752
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spelling	RepoAGROSAVIA407522025-03-06T03:00:18Z Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life Herrera, Santiago Reyes Herrera, Paula H. Shank, Timothy M. Investigación agropecuaria - A50 Árbol Genoma Enzima Diseño experimental Transversal http://aims.fao.org/aos/agrovoc/c_7887 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_2603 http://aims.fao.org/aos/agrovoc/c_29466 High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes – generically known as restriction-site associated DNA sequencing (RAD-seq) – is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is a knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for non-model species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition-sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting ‘neutral’ elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced-representation data is available (including transcriptomes and ‘neutral’ RAD-seq datasets). 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Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life

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