An Illumina approach to MHC typing of Atlantic salmon

Sundaram, Arvind; Garseth, Åse Helen; Maccari, Giuseppe; Grimholt, Unni

doi:10.1007/s00251-019-01143-8

Cited by 9 publications

(8 citation statements)

References 58 publications

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“…Sequence data from Illumina were analysed as described in (38). Briefly, raw sequence data was cleaned to remove/trim low quality data, adapter sequences and PhiX (Illumina spike-in) using BBDuk v34.56 (part of BBTools; https://jgi.doe.gov/dataand-tools/bbtools/bb-tools-user-guide/).…”

Section: Bioinformaticsmentioning

confidence: 99%

Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel

et al. 2022

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Protective cellular immune responses have been difficult to study in fish, due to lack of basic understanding of their T cell populations, and tools to study them. Cellular immunity is thus mostly ignored in vaccination and infection studies compared to humoral responses. High throughput sequencing, as well as access to well assembled genomes, now advances studies of cellular responses. Here we have used such resources to describe organization of T cell receptor beta genes in Atlantic salmon. Salmonids experienced a unique whole genome duplication approximately 94 million years ago, which provided these species with many functional duplicate genes, where some duplicates have evolved new functions or sub-functions of the original gene copy. This is also the case for T cell receptor beta, where Atlantic salmon has retained two paralogue T cell receptor beta regions on chromosomes 01 and 09. Compared to catfish and zebrafish, the genomic organization in both regions is unique, each chromosomal region organized with dual variable- diversity- joining- constant genes in a head to head orientation. Sequence identity of the chromosomal constant sequences between TRB01 and TRB09 is suggestive of rapid diversification, with only 67 percent as opposed to the average 82-90 percent for other duplicated genes. Using virus challenged samples we find both regions expressing bona fide functional T cell receptor beta molecules. Adding the 292 variable T cell receptor alpha genes to the 100 variable TRB genes from 14 subgroups, Atlantic salmon has one of the most diverse T cell receptor alpha beta repertoire of any vertebrate studied so far. Perhaps salmonid cellular immunity is more advanced than we have imagined.

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Section: Bioinformaticsmentioning

confidence: 99%

Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel

et al. 2022

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“…Trimmed read pairs (TRIMMOMATIC, Bolger et al 2014) were mapped to the pool assembly using BWA-MEM (Li 2013) to con rm proximity, ltered by quality using SAMTOOLS , and duplicates removed with SAMBAMBA (Tarasov et al 2015) before fusing into individual phased sequence reads, sometimes called merged reads or "FLASHed reads" (Bushnell et al 2017;Sundaram et al 2020). If read pairs were proximal and oriented correctly but were nonoverlapping then the intervening region was padded with a string of Ns of a length predicted from pool assembly contigs.…”

Section: Methodsmentioning

confidence: 99%

A Pan-Genome Data Structure Induced by Pooled Sequencing Facilitates Variant Mining in Heterogeneous Germplasm

Reeves

Richards²

2022

Preprint

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Valuable genetic variation lies unused in gene banks due to the difficulty of exploiting heterogeneous germplasm accessions. Advances in molecular breeding, including transgenics and genome editing, present the opportunity to exploit hidden sequence variation directly. Here we describe the pangenome data structure induced by wholegenome sequencing of pooled individuals from wild populations of Patellifolia spp., a source of disease resistance genes for the related crop species sugar beet (Beta vulgaris). We represent the pangenome of a heterogeneous population sample as a set of phased reads mapped to a reference genome assembly derived from the sequence pool or other sources. We show that this basic data structure can be queried by homology to identify short haplotypic variants present in the wild relative, at genes of agronomic interest in the crop. Further we demonstrate the possibility of cataloging short haplotypic variation in all Patellifolia genomic regions that have corresponding single copy orthologous regions in sugar beet. The data structure, termed a "phased read archive", can be produced, altered, and queried using standard tools to facilitate discovery of agronomicallyimportant sequence variation in heterogeneous germplasm.

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Section: Methodsmentioning

confidence: 99%

A pan-genome data structure induced by pooled sequencing facilitates variant mining in heterogeneous germplasm

Reeves

Richards

2022

Mol Breeding

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Valuable genetic variation lies unused in gene banks due to the di culty of exploiting heterogeneous germplasm accessions. Advances in molecular breeding, including transgenics and genome editing, present the opportunity to exploit hidden sequence variation directly. Here we describe the pangenome data structure induced by wholegenome sequencing of pooled individuals from wild populations of Patellifolia spp., a source of disease resistance genes for the related crop species sugar beet (Beta vulgaris). We represent the pangenome of a heterogeneous population sample as a set of phased reads mapped to a reference genome assembly derived from the sequence pool or other sources. We show that this basic data structure can be queried by homology to identify short haplotypic variants present in the wild relative, at genes of agronomic interest in the crop. Further we demonstrate the possibility of cataloging short haplotypic variation in all Patellifolia genomic regions that have corresponding single copy orthologous regions in sugar beet. The data structure, termed a "phased read archive", can be produced, altered, and queried using standard tools to facilitate discovery of agronomicallyimportant sequence variation in heterogeneous germplasm.

show abstract

An Illumina approach to MHC typing of Atlantic salmon

Cited by 9 publications

References 58 publications

Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel

Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel

A Pan-Genome Data Structure Induced by Pooled Sequencing Facilitates Variant Mining in Heterogeneous Germplasm

A pan-genome data structure induced by pooled sequencing facilitates variant mining in heterogeneous germplasm

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