An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

Abstract

Background: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual. Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Successive Losses of Central Immune Genes Characterize the Gadiformes’ Alternate Immunity

“…These sequences were used in TBLASTN searches as described above but with options “outfmt 6” and “sseq” and were readily detected in the unitig datasets. Partial synteny was obtained for 15 of 38 non-reference teleosts harboring Mx and for two of 25 species not harboring Mx (not counting Atlantic cod as the new version of the Atlantic cod genome was investigated; Tørresen et al 2016). The same approach was also applied for TLR5 .…”

“…Furthermore, for TLR5 the leader domain and TIR domain were used as queries alone in addition to the full length TLR5 sequence as these domains often were located to other unitigs than the main part of the query sequence (supplementary tables S3 and S4, Supplementary Material online). Partial synteny was found for Thunnus albacares and Helostoma temminckii (contains TLR5 ) as well as in Laemonema laureysi (no TLR5 ) (not counting Atlantic cod as the new version of the Atlantic cod genome was investigated; Tørresen et al 2016). Finally, for TLR5 we extracted the TLR5 sequences from species neighboring P. fuscus , Lampris guttatus , and Regalecus glesne to ensure that our original query TLR5 sequences did not miss any potential TLR5 genes in these species.…”

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

“…The ancient read data were processed by using PALEOMIX (83). In short, forward and reverse reads were collapsed with AdapterRemoval v1.5 (84) and aligned to the Gadmor2 reference (85,86) by using BWA aln v.0.7.5a-r405 (87). The modern data were aligned by using BWA mem.…”

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

“…Hierarchical methods do not require a secondary technology and instead use multiple rounds of read overlapping (alignment) and correction to improve the quality of the single-molecule reads prior to assembly (Chin et al 2013;Koren et al 2013). Finally, direct methods attempt to assemble single-molecule reads from a single overlapping step without any prior correction (Li 2016;Tørresen et al 2017). All three approaches are capable of producing an accurate final assembly.…”