Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids.

Mark F Richardson,Fahad Alshanbari,Polina Perelman,Kylie Munyard,Belinda Appleton,Felicity Jackling,Ahmed Tibary,Rhys Cransberg,Theodore R Allnutt,Gus A Wright,Larry J Croft,Terje Raudsepp,Matthew Jevit

doi:10.3389/fgene.2019.00586

Abstract

The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.

Highlights

Alpacas and llamas were domesticated in the high Andes around 9,000 years ago and have been associated with humans for as long as cattle, horses and dogs (Wheeler, 1995; Bruford et al, 2003)
We considered scaffolds anchored when the primers uniquely mapped to one scaffold and the primers mapped in the correct orientation
Procurement of blood and tissue samples followed the United States Government Principles for the Utilization and Care of Vertebrate Animals Used in Testing, Research and Training

Summary

Introduction

Alpacas and llamas were domesticated in the high Andes around 9,000 years ago and have been associated with humans for as long as cattle, horses and dogs (Wheeler, 1995; Bruford et al, 2003). Alpacas are gaining popularity worldwide, mainly for their high quality fiber, and as a docile companion species. Alpacas and camelids in general, are species of broader interest for several fields in biology and biomedical sciences. All camelids are uniquely adapted to extreme environments – the New World species to high altitude and the Old World camels to arid desert environments (Wu et al, 2014), due to these adaptations their genomes may reveal important signatures of natural or human selection. Camelids are of biomedical interest because of the presence of small and functionally efficient heavy chain-only antibodies, which are not found in other mammalian groups (Flajnik et al, 2011; Griffin et al, 2014; Cohen, 2018)

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