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Methods Mol Biol. 2017;1650:47-67. doi: 10.1007/978-1-4939-7216-6_3.

A Step-by-Step Guide to Assemble a Reptilian Genome.

Author information

1
Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland.
2
SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
3
Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
4
Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany.
5
Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland. athanasia.tzika@unige.ch.
6
SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. athanasia.tzika@unige.ch.
7
Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. athanasia.tzika@unige.ch.

Abstract

Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.

KEYWORDS:

Corn snake; DNA extraction; Genome assembly; Genome sequencing; Genomics; Optical mapping; Snake genome; Transcriptome

PMID:
28809013
DOI:
10.1007/978-1-4939-7216-6_3
[Indexed for MEDLINE]

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