Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

Halie Rando,Zijun Xiong,Guojie Zhang,Shaohong Feng,Michael Robson,Marta Farré,Denis Larkin,Estelle Bastounes,Ronak Buch,Jennifer Johnson,Shiping Liu,Anna Kukekova,Lyudmila Trut,Xueyan Xiang,Naomi Won,Jaebum Kim

doi:10.3390/genes9060308

Abstract

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Highlights

IntroductionAt the turn of the millennium, the potential for mammalian comparative genomics to offer significant insights into both basic (e.g., adaptation and species formation) and applied (e.g., biomedical and agricultural) biology was already apparent [1]
At the turn of the millennium, the potential for mammalian comparative genomics to offer significant insights into both basic and applied biology was already apparent [1]
With 40-Kbp block resolution, Reference-Assisted Chromosome Assembly (RACA) identified 537 conserved blocks ranging in size from 41.4 Kbp to 54.7 Mbp of fox sequence, with sizes of the blocks ranging from 42.3 Kbp to 53.8 Mbp in the dog

Summary

Introduction

At the turn of the millennium, the potential for mammalian comparative genomics to offer significant insights into both basic (e.g., adaptation and species formation) and applied (e.g., biomedical and agricultural) biology was already apparent [1]. The original mammalian genome sequencing projects targeted popular model species such as human [2,3] and mouse [4]. Initial interest in comparative mammalian genomics was catalyzed by the recognized potential for comparative analysis to reveal regions of evolutionary constraint and to support the annotation of the human genome, but the high costs associated with genome assembly using Sanger sequencing technology limited the original comparative assembly project to the assembly of genomes from only 29 eutherian mammals [5]. The effect of NGS technology on the scope of mammalian genomics is manifest in the 10K Genomes

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Conclusion