Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable ...structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. Here we assess this by using long-read sequencing platforms from PacBio and Oxford Nanopore, supplemented with short-read sequencing and Bionano optical mapping, to sequence DNA extracted from CD14
+
monocytes and peripheral blood mononuclear cells from a single European individual identified as HV31. We use this data to build a
de novo
assembly of eight genomic regions encoding four key components of the immune system, namely the human leukocyte antigen, immunoglobulins, T cell receptors, and killer-cell immunoglobulin-like receptors. Validation of our assembly using k-mer based and alignment approaches suggests that it has high accuracy, with estimated base-level error rates below 1 in 10 kb, although we identify a small number of remaining structural errors. We use the assembly to identify heterozygous and homozygous structural variation in comparison to GRCh38. Despite analyzing only a single individual, we find multiple large structural variants affecting core genes at all three immunoglobulin regions and at two of the three T cell receptor regions. Several of these variants are not accurately callable using current algorithms, implying that further methodological improvements are needed. Our results demonstrate that assessing haplotype variation in these regions is possible given sufficiently accurate long-read and associated data. Continued reductions in the cost of these technologies will enable application of these methods to larger samples and provide a broader catalogue of germline structural variation at these loci, an important step toward making these regions accessible to large-scale genetic association studies.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Background
The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in ...coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management.
Findings
Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.
Conclusions
The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
We present a genome assembly from a clonal population of
Eimeria tenella
Houghton parasites
(Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The ...entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.
We present a genome assembly from an individual male
Rattus norvegicus
(the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the ...assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for
R. norvegicus
and has been adopted by the Genome Reference Consortium.
We present a genome assembly from an individual female
Salmo trutta
(the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of ...the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
We present a genome assembly from an individual female
Aquila chrysaetos chrysaetos
(the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The ...majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
We present a genome assembly from an individual male
(the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span. The majority of the assembly ...is scaffolded into 18 chromosomal pseudomolecules, including the X sex chromosome. Gene annotation of this assembly on Ensembl has identified 21,394 protein coding genes.
We present a genome assembly from an individual male
(the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of ...the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.
We present a genome assembly from an individual male
(the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of ...the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
We present a genome assembly from an individual male
(the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of ...the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
PDF
