Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

Abstract

Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate‐pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi‐C and Dovetail Genomics Chicago libraries and long‐read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high‐quality contiguous reference genome is the dromedary ( Camelus dromedarius ). Draft genomes exist but are highly fragmented, and a high‐quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi‐C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome‐level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi‐C libraries increased the longest scaffold over 12‐fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50‐fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long‐read sequencing.

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

“…Pacific Biosciences (PacBio) sequencing is the most commonly used third-generation sequencing technology generating long reads, its accuracy remains inferior to that of the second-generation Illumina sequencing technology (Tedersoo, Tooming-Klunderud & Anslan, 2018). Therefore, increasing attention has been paid to the combination of PacBio and Illumina techniques for genome assembly (Elbers et al, 2019).…”

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

“…In the CamDro3 annotation, we predicted 22,917 genes that produced 34,135 proteins, and 7.4 % (1,705) of genes had no assigned annotation. These numbers are slightly higher than for the CamDro2 assembly for which we had predicted 22,534 genes that produced 34,024 proteins, and 7.7 % (1,730) of genes had no assigned annotation [11]. We assessed if predicted proteins were truncated due to uncorrected indels introduced by PacBio reads by comparing the predicted protein length hit distribution of the CamDro1 assembly (Illumina only data, Figure 1, red line), which should lack such PacBio speci c error, to that of the CamDro2 (Figure 1, green line) and CamDro3 assemblies ( Figure 1, blue line).…”

“…Next, the Chicago assembly was scaffolded with Hi-C data. Using a PacBio Sequel sequencer, 11x long-read coverage were generated ( [11]; Sequence Read Archive (SRA) accession: SRP050586) and PBJelly [39] was used to ll in gaps in the Hi-C assembly. PBJelly assembly was polished with Pilon [40] employing the same trimmed and errorcorrected Illumina short-insert sequences used for the de novo assembly of CamDro1 by Fitak et al ( [8]; SRA accession: SRR2002493).…”

Chromosome‐level assembly of wild Bactrian camel genome reveals organization of immune gene loci

“…The PacBio assembly comprised 4,402 contigs totalling 2.09 Gb, which possessed an N50 of 5.37 Mb (Table 1). The continuity of our PacBio assembly was not only dramatically improved compared to that of CB1 and MBC1 ( Figure S2), but was also better than some other genome assemblies that were based on long-read sequencing (Bickhart et al, 2017;Gordon et al, 2016;Jain et al, 2018), including the improved version of the dromedary genome (CamDro2) (Elbers et al, 2019). To reduce the base errors within the assembly, we polished the contigs using both the PacBio reads and Illumina reads.…”

“…Additionally, new scaffolding technology such as chromatin interaction mapping (Hi-C) allowed the contigs to be assembled to the scale of full chromosomes (Bickhart et al, 2017;Burton et al, 2013). Recently, Hi-C technology and low-coverage long-read sequencing (11×) were applied to upgrade the short-read assembly of the dromedary (Elbers et al, 2019). Based on the upgraded assembly, the genomic organization of natural killer cell receptor genes in camels was characterized (Futas et al, 2019).…”