Dataset Information

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

ABSTRACT: The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9?Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.

SUBMITTER: Fuselli S

PROVIDER: S-EPMC6133961 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

Fuselli S S Baptista R P RP Panziera A A Magi A A Guglielmi S S Tonin R R Benazzo A A Bauzer L G LG Mazzoni C J CJ Bertorelle G G

Heredity 20180324 4

The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utiliz ...[more]

PMID: 29572469

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Project description:BACKGROUND: In mammals, males typically have shorter lives than females. This difference is thought to be due to behavioural traits which enhance competitive abilities, and hence male reproductive success, but impair survival. Furthermore, in many species males usually show higher parasite burden than females. Consequently, the intensity of selection for genetic factors which reduce susceptibility to pathogens may differ between sexes. High variability at the major histocompatibility complex (MHC) genes is believed to be advantageous for detecting and combating the range of infectious agents present in the environment. Increased heterozygosity at these immune genes is expected to be important for individual longevity. However, whether males in natural populations benefit more from MHC heterozygosity than females has rarely been investigated. We investigated this question in a long-term study of free-living Alpine chamois (Rupicapra rupicapra), a polygynous mountain ungulate. RESULTS: Here we show that male chamois survive significantly (P = 0.022) longer if heterozygous at the MHC class II DRB locus, whereas females do not. Improved survival of males was not a result of heterozygote advantage per se, as background heterozygosity (estimated across twelve microsatellite loci) did not change significantly with age. Furthermore, reproductively active males depleted their body fat reserves earlier than females leading to significantly impaired survival rates in this sex (P < 0.008). This sex-difference was even more pronounced in areas affected by scabies, a severe parasitosis, as reproductively active males were less likely to survive than females. However, we did not find evidence for a survival advantage associated with specific MHC alleles in areas affected by scabies. CONCLUSIONS: Increased MHC class II DRB heterozygosity with age in males, suggests that MHC heterozygous males survive longer than homozygotes. Reproductively active males appear to be less likely to survive than females most likely because of the energetic challenge of the winter rut, accompanied by earlier depletion of their body fat stores, and a generally higher parasite burden. This scenario renders the MHC-mediated immune response more important for males than for females, which implies a relatively stronger selection pressure on MHC genes in males than in females.

Project description:Global warming is considered as a phenomenon having a negative effect on animals living in cold climate. However, herbivorous species inhabiting cold zones may potentially benefit from increase of temperature as this influence duration of vegetation period and increase food resources. In this study, we analyze the impact of climate factors on the long-term dynamics of an isolated and unhunted population of the Tatra chamois Rupicapra rupicapra tatrica. The population growth rate, based on autumnal chamois counting carried out from 1957 to 2016, were correlated with a set of climatic variables. We tested the hypothesis that high temperatures in summer could have a positive impact on the population, since they influence vegetation growth, which ensure food resources. On the other hand, heavy falls of snow and long-lasting and deep snow cover could adversely affect the population by reducing population survival during the winter. The results of this study indicate that climatic variables best explaining the autoregressed population growth rate (from the autumn of year t-1 to the autumn of year t) were the mean summer temperature of year t-1: the population increase was greater following a warmer summer in year t-1 and, in lower extent, the total precipitation during winter: the population decrease was greater following a winter with heavy snowfall. Duration and thickness of snow cover have no negative effect on population growth rate. The results indicate that the population dynamic of the Tatra chamois is determined in the long term by weather conditions, mainly by temperature, when kids are birthing and growing. The results of this work highlight that climatic changes may be responsible for the population dynamic of high-mountain species. Climate warming may lead to increase in duration of vegetation period in cold climatic zones, what may in turn have positive effect on herbivorous species, which relay upon food resources limited by low temperatures within vegetation period.

Dataset Information

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

Publications

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

Similar Datasets

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