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Recombination and degeneration of a neo-sex chromosome: a RAD-analysis of the great reed warbler, Acrocephalus arundinaceus

Lundqvist, Martin (2015) MOBT19 20142
Degree Projects in Molecular Biology
Abstract
Sex chromosome evolution is a fascinating research topic because sex chromosomes provide a snapshot of evolution in many different lineages. Sex chromosomes often cease to recombine and therefore degenerate, and have also often been reshuffled during their evolution from autosomes. It has been discovered that within Sylvioidea passerine species half of chromosome 4a has translocated and fused with the Z chromosome forming a neo-sex chromosome. Large-scale sequence data, so called restriction-site associated DNA (RAD) tag sequencing data, from great reed warbler, Acrocephalus arundinaceus, from lake Kvismaren, Sweden, was analyzed in order to examine the translocation in greater detail. Nearly a terabyte of paired-end reads was checked for... (More)
Sex chromosome evolution is a fascinating research topic because sex chromosomes provide a snapshot of evolution in many different lineages. Sex chromosomes often cease to recombine and therefore degenerate, and have also often been reshuffled during their evolution from autosomes. It has been discovered that within Sylvioidea passerine species half of chromosome 4a has translocated and fused with the Z chromosome forming a neo-sex chromosome. Large-scale sequence data, so called restriction-site associated DNA (RAD) tag sequencing data, from great reed warbler, Acrocephalus arundinaceus, from lake Kvismaren, Sweden, was analyzed in order to examine the translocation in greater detail. Nearly a terabyte of paired-end reads was checked for intact barcodes, RAD-cutsites and reduced according to exactly matching pairs of reads, before being aligned to the genome of zebra finch, Taeniopygia guttata. After alignment the main components within the program Stacks were run, in order to build the loci within the population into a catalog and match all samples to that catalog, but the results proved unusable because of large amounts of homozygosity and a very low allele Stacks depth. IGV (Integrative Genomic Viewer) enabled visual examination along genomes of particular families within the dataset, and for a subset of loci single-nucleotide polymorphisms were scored. These SNPs were used in Crimap to construct a linkage map for parts of the Z chromosome and neo-sex part of chromosome 4a. This showed that at least one inversion has occurred within a sequence on the neo-sex chromosome, and that the fusion point between the neo-sex and the ancestral sex chromosome might be located in the central part of the neo-sex chromosome. Moreover, sequencing depth coverage was examined in a subset of individuals to evaluate whether the W chromosome has been degenerating. Among females (ZW), but not among males (ZZ), the proportion of mapped reads on the Z chromosome was considerably lower than for autosomal chromosomes (AA). However, this difference between sexes was smaller for the neo-sex chromosome than for the ancestral sex chromosome. This indicates that the neo-sex part of the W chromosome is in an intermediate stage of degeneration. I conclude that an inversion has been detected which affects the interpretation of how the fusion has occurred, and that the degree of coverage among females seems to be in agreement with comparable female heterogametic systems. (Less)
Popular Abstract
A study of a new sex chromosomes in great reed warbler

The study of evolution is in some respects, similar to astronomy; the processes studied and whose history one attempts to trace are orders of magnitude longer than any human life. However, the evolution of sex chromosomes can sometimes be seen as a snapshot of evolution in progress. Sex chromosomes have degenerated during evolution (the short and comparatively gene-less Y chromosome being an example of this), and often been reshuffled during their evolution from autosomes (the body chromosomes).

Bird genomes tend to be quite stable over evolutionary time periods, compared to mammalian genomes. Their rates of fissions, fusions and inversions have been estimated to be up to ten... (More)
A study of a new sex chromosomes in great reed warbler

The study of evolution is in some respects, similar to astronomy; the processes studied and whose history one attempts to trace are orders of magnitude longer than any human life. However, the evolution of sex chromosomes can sometimes be seen as a snapshot of evolution in progress. Sex chromosomes have degenerated during evolution (the short and comparatively gene-less Y chromosome being an example of this), and often been reshuffled during their evolution from autosomes (the body chromosomes).

Bird genomes tend to be quite stable over evolutionary time periods, compared to mammalian genomes. Their rates of fissions, fusions and inversions have been estimated to be up to ten times lower than in mammals. Changes in the overall structure of bird genomes are therefore fascinating, since these changes are comparatively rare. Unlike humans, where males are XY (the heterogametic sex) and females XX (the homogametic sex), birds have a ZW sex chromosome system, where males are homogametic with ZZ and females heterogametic with ZW. It has previously been discovered that within Sylvioidea passerine species half of chromosome 4a has broken off and fused with the sex chromosome Z forming a so-called neo-sex chromosome.

One member of the Sylvioidea passerines is the great reed warbler, a long-distance migrant that winters in sub-Saharan Africa but breeds in reed lakes in Europe and western Asia. One such breeding place is Lake Kvismaren in south Central Sweden. The study population was founded by a handful of individuals in 1978 and has been studied ever since 1983. 270 great reed warbler individuals were used in this study. So-called linkage maps have been made of the fused Z-4a chromosomes in previous studies. In order to be able to make a linkage map, you need to have the genomes of the individuals you are examining aligned to the genome of the species - or the nearest related model species, in this case the zebra finch. In this study, a lot of genomic sequence data from 270 great reed warbler individuals was aligned to the zebra finch genome and eight families with a total of 52 individuals were chosen as a foundation for a new and detailed linkage map. Only families with a large number of offspring and consisting of individuals with a lot of data were included.

After many analyses and visual examination of the entire 4a and Z chromosomes (using a visualization tool for genomic datasets called Integrative Genomics Viewer) informative polymorphisms were used as the foundation for a new linkage map. The interesting thing about the new linkage map was that it suggests that not only has there been a fusion between Z and 4a as detected previously, but, judging by the order of the markers detected, there has been an inversion within this neo-sex chromosome!

Advisor: Bengt Hansson
Master’s Degree Project in Molecular Biology 60 credits 2015
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Lundqvist, Martin
supervisor
organization
course
MOBT19 20142
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8891630
date added to LUP
2016-09-13 15:33:37
date last changed
2016-09-13 15:39:27
@misc{8891630,
  abstract     = {Sex chromosome evolution is a fascinating research topic because sex chromosomes provide a snapshot of evolution in many different lineages. Sex chromosomes often cease to recombine and therefore degenerate, and have also often been reshuffled during their evolution from autosomes. It has been discovered that within Sylvioidea passerine species half of chromosome 4a has translocated and fused with the Z chromosome forming a neo-sex chromosome. Large-scale sequence data, so called restriction-site associated DNA (RAD) tag sequencing data, from great reed warbler, Acrocephalus arundinaceus, from lake Kvismaren, Sweden, was analyzed in order to examine the translocation in greater detail. Nearly a terabyte of paired-end reads was checked for intact barcodes, RAD-cutsites and reduced according to exactly matching pairs of reads, before being aligned to the genome of zebra finch, Taeniopygia guttata. After alignment the main components within the program Stacks were run, in order to build the loci within the population into a catalog and match all samples to that catalog, but the results proved unusable because of large amounts of homozygosity and a very low allele Stacks depth. IGV (Integrative Genomic Viewer) enabled visual examination along genomes of particular families within the dataset, and for a subset of loci single-nucleotide polymorphisms were scored. These SNPs were used in Crimap to construct a linkage map for parts of the Z chromosome and neo-sex part of chromosome 4a. This showed that at least one inversion has occurred within a sequence on the neo-sex chromosome, and that the fusion point between the neo-sex and the ancestral sex chromosome might be located in the central part of the neo-sex chromosome. Moreover, sequencing depth coverage was examined in a subset of individuals to evaluate whether the W chromosome has been degenerating. Among females (ZW), but not among males (ZZ), the proportion of mapped reads on the Z chromosome was considerably lower than for autosomal chromosomes (AA). However, this difference between sexes was smaller for the neo-sex chromosome than for the ancestral sex chromosome. This indicates that the neo-sex part of the W chromosome is in an intermediate stage of degeneration. I conclude that an inversion has been detected which affects the interpretation of how the fusion has occurred, and that the degree of coverage among females seems to be in agreement with comparable female heterogametic systems.},
  author       = {Lundqvist, Martin},
  language     = {eng},
  note         = {Student Paper},
  title        = {Recombination and degeneration of a neo-sex chromosome: a RAD-analysis of the great reed warbler, Acrocephalus arundinaceus},
  year         = {2015},
}