TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Cécile Monat,Axel Himmelbach,Manuel Spannagl,Chengdao Li,Robbie Waugh,Martin Mascher,Jennifer Ens,Curtis Pozniak,Heidrun Gundlach,Klaus F X Mayer,Thomas Lux,Nils Stein,Gary J Muehlbauer,Sudharsan Padmarasu,Alan H Schulman,Uwe Scholz,Ilka Braumann,Thomas Wicker

doi:10.1186/s13059-019-1899-5

Abstract

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

Highlights

The Triticeae species wheat and barley were among the founder crops of Neolithic agriculture in Western Asia and continue to dominate agriculture in temperate regions of the world to the present day
Chromosome-scale reference sequence assemblies have come available for barley (Hordeum vulgare) [3], hexaploid bread wheat (Triticum aestivum) [4], and tetraploid durum wheat (T. turgidum ssp. durum) [5] as well as the wheat wild relatives Aegilops tauschii [6], T. urartu [7], and T. turgidum ssp. dicoccoides [8]
Assembling bacterial artificial chromosomes (BACs) guided by a physical map yielded megabase-sized scaffolds [3, 11], which were arranged into chromosomal superscaffolds by long-range linkage information afforded by ultra-dense genetic maps [12, 13], chromosome conformation capture sequencing (Hi-C) [14, 15], or Bionano optical mapping [16]

Summary

Introduction

The Triticeae species wheat and barley were among the founder crops of Neolithic agriculture in Western Asia and continue to dominate agriculture in temperate regions of the world to the present day. High content of transposable elements (TEs), and polyploidy (in the case of wheat) have long impeded genome assembly projects in the Triticeae [1, 2]. Chromosome-scale reference sequence assemblies have come available for barley (Hordeum vulgare) [3], hexaploid bread wheat (Triticum aestivum) [4], and tetraploid durum wheat Durum) [5] as well as the wheat wild relatives Aegilops tauschii (wheat D genome progenitor) [6], T. urartu (wheat A genome progenitor) [7], and T. turgidum ssp. Assembling bacterial artificial chromosomes (BACs) guided by a physical map yielded megabase-sized scaffolds [3, 11], which were arranged into chromosomal superscaffolds (so-called pseudomolecules) by long-range linkage information afforded by ultra-dense genetic maps [12, 13], chromosome conformation capture sequencing (Hi-C) [14, 15], or Bionano optical mapping [16]. BAC-byBAC assembly is laborious and time-consuming [3] and has become an obsolete method of sequence assembly

Methods

Results

Conclusion