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Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. This giant chromosome functions as a sex chromosome in some of these species.

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We test two hypotheses of how this giant sex chromosome may have evolved. The first hypothesis proposes that it evolved by accumulating repetitive elements as recombination was reduced around a dominant sex determination locus, as suggested by canonical models of sex chromosome evolution. An alternative hypothesis is that the giant sex chromosome originated via the fusion of an autosome with a highly repetitive B chromosome, one of which carried a sex determination locus.

We test these hypotheses using comparative analysis of chromosome-scale cichlid and teleost genomes. We find that the giant sex chromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome.

Comparisons across 69 teleost genomes reveal that the giant sex chromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long noncoding RNAs.

The favor sex with giant B chromosome fusion hypothesis for the origin of the giant chromosome. Almost two centuries of cytogenetic studies have revealed the great diversity of animal karyotypes. Chromosome s can differ dramatically among closely related species even without changes in ploidy Yang et al. Although the total length of the chromosomes is directly related to genome size, and thus to factors such as population size Lynch and Conerythere is little theory to explain why chromosome s should vary so dramatically.

There are also dramatic differences among species in the shapes of chromosomes. Some lineages contain mostly acrocentric chromosomes, whereas others segregate mostly metacentric chromosomes. Differences among species have been attributed to supposedly random processes of chromosome fusion and fission. In some cases, fusion events have left behind a trace of interstitial telomere sequences ITSssuch as human chromosome 2 Ijdo et al.

Recent data suggest that these differences in fusions and fission events may arise from changing biases in centromeric drive during female meiosis Molina et al.

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Additional forces such as mutation rates, population structure, drift, recombination, and gene expression may also contribute to these differences Qumsiyeh sex with giant Dobigny et al. We suspect there might be some common mechanisms and rules governing the variety of sizes and shapes of chromosomes in a particular lineage. However, at present, we are unable to predict the structure of karyotypes—meaning the and shape acrocentric vs.

The genome is a battleground on which genetic conflicts are fought on many levels. Selfish genetic elements such as transposons tend to proliferate, increasing the size of genomes Canapa et al. Centromeres compete for transmission through meiosis Malik Many of these conflicts involve selfish elements that drive i. Such selfish genetic elements often impose a cost on fitness, including transposon insertions that render genes nonfunctional Werrenand deleterious alleles that have hitchhiked to high frequency via linkage with a driving centromere Fishman and Kelly These selfish chromosomes develop mechanisms to favor their transmission, despite a potential negative impact on organismal fitness Meiklejohn and Tao B chromosomes are highly repetitive, largely heterochromatic, contain many transposable elements, pseudogenes, and noncoding RNAs.

Recent work has shown that B chromosomes also often contain many functional genes that are transcribed which can affect transcriptome regulation in various tissues and ultimately may change observable phenotypes Makunin et al.

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Sex chromosomes are another focal point for genetic conflicts. Sexually antagonistic selection favors a reduction in recombination on sex chromosomes to increase the association of sexually antagonistic alleles with the sex-determining locus Charlesworth ; Charlesworth et al. Successive events reducing recombination e. Alternative sex with giant for the restriction of recombination on sex chromosomes include meiotic drive, heterozygote advantage, and genetic drift Ponnikas et al. Sexual conflicts are common and often drive the evolution and turnover of sex chromosomes Parker ; Chapman et al.

It has been proposed that female meiotic drive contributes to the evolution of new sex chromosomes via fusions with autosomes, and that karyotype shape affects the types of fusions that occur Yoshida and Kitano In fishes and reptiles, sex chromosome—autosome fusions more often involve Y chromosomes than X, W, or Z chromosomes, which is consistent with these Y-fusion events being slightly deleterious and fixed by genetic drift Pennell et al.

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It has been suggested that some sex chromosomes originated from B chromosomes, or vice versa, based on similarities in their repetitive DNA and transposons, lack of recombination, patterns of heterochromatic gene silencing, and dearth of functional genes Hackstein et al. However, evidence to support these hypotheses is limited Charlesworth et al.

Definitive tests of these hypotheses will require data from closely related species, as both B chromosomes and young sex chromosomes evolve quite rapidly. Cichlid sex with giant have undergone an extraordinary radiation in East Africa, diversifying into more than 1, species over the last 25 MY Kocher Cichlid karyotypes vary and B chromosomes have now been discovered in numerous cichlid species Poletto, Ferreira, and Martins ; Valente et al. Many Lake Malawi cichlid species harbor a B chromosome that is present as a single copy and only in females.

This B chromosome carries an epistatically dominant female W sex-determiner, which likely evolved to promote the transmission of the B chromosome through female meiosis Clark et al. The Lake Victoria B chromosome can be found in one to three copies in males or females, and typically shows no effect on the phenotype Poletto, Ferreira, and Martins ; Valente et al. However, in one species of Lake Victoria cichlids, B chromosomes were shown to have an effect on sex determination Yoshida et al.

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Both the Victoria and Malawi B chromosomes have been characterized cytogenetically Poletto, Ferreira, and Martins ; Fantinatti et al. Similar to other well-studied B chromosomes, these cichlid B chromosomes are highly repetitive Valente et al.

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Many of these blocks contain transcribed genes involved in processes related to meiosis and mitosis, suggesting that genes on these B chromosomes may be involved in ongoing conflicts to maintain the B chromosomes in the population Valente et al. Studies of African cichlids also have revealed an extraordinary diversity of sex chromosomes, and the highest rate of sex chromosome turnover among vertebrates Gammerdinger and Kocher ; Vicoso Genetic conflicts have contributed to at least some of this diversity.

For example, sexual conflict involving color polymorphisms led to the evolution of a novel W sex chromosome Roberts et al. Most cichlid sex chromosomes are homomorphic and were therefore identified using sequence markers Lee et al. Whole-genome sequencing techniques are allowing for the rapid discovery of additional cichlid sex chromosomes Gammerdinger et al.

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Several of these novel sex chromosomes involve chromosome fusions Gammerdinger et al. Additional work revealed that African cichlids have experienced two relatively recent chromosome fusions of ancient vertebrate chromosomes Liu et al. In Astatotilapia burtonia sex chromosome is found on LG, a chromosome fusion that is not found in other cichlid species Roberts et al.

The A. This giant chromosome, referred to here as linkage group 3 LG3comprises at least LG3 carries a WZ sex determination locus in several species including the blue tilapia, O. The LG3 giant chromosome is retained in oreochromines, even when sex determination is controlled by loci on other chromosomes, such as LG1 and LG23 Eshel et al. A LG3 giant sex chromosome has also been observed in several closely related cichlid lineages including Pelmatolapia Tilapia mariae Gammerdinger et al.

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Figure 1 provides an overview of karyotype evolution in cichlids, as well as the distribution of fusion events, the LG3 giant sex chromosome, and B chromosomes in species from Lake Malawi and Lake Victoria. Summary of major karyotype evolution across the phylogeny of cichlids. The Oreochromini sex with giant several additional lineages harbor the LG3 giant chromosome. The LG3 giant chromosome acts as a WZ sex chromosome in at least three different species of Oreochromis as well as additional lineages such as Pelmatolapia mariae.

Karyotypes are adapted with permission Poletto, Ferreira, Cabral-de-Mello, et al. We considered two hypotheses for the origin of the LG3 giant sex chromosome. The first model is that an ancestral autosome acquired a sex-determining allele. Following the canonical model of sex chromosome evolution, selection would favor a reduction in recombination e. This reduction in recombination would allow an accumulation of deleterious alleles and repetitive elements Charlesworth et al.

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Under this model, the giant sex chromosome should show conserved synteny with the ancestral autosome, except where gene order has been altered by inversions. The second model proposed here is that the LG3 giant sex chromosome arose by fusion of a highly repetitive B chromosome with another chromosome.

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Either chromosome could have been carrying a sex determination locus prior to sex with giant. The B chromosome may have carried a sex determination locus to favor its transmission through meiotic drive. This has been shown in Lake Malawi cichlid species where a W sex determination locus likely evolved to enhance the meiotic drive of the B chromosome that carries it since this W is dominant to a separate XY locus Clark and Kocher Such a fusion might be favored if it associated sexually antagonistic variation with the sex determiner, or if it contributed to the drive of the B chromosome.

Alternatively, the other chromosome may have carried a sex determination locus and fusion was favored because of a sexually antagonistic locus on the B chromosome. In either case, major portions of the giant sex chromosome would show no ificant synteny with the ancestral autosome due to the fusion with a B chromosome. Here, we test these hypotheses through a comparative genomic analysis of many cichlid and teleost fish genomes. We present characterizing the giant sex chromosome in the Oreochromini by analyzing synteny, recombination, repeat content, and gene ampliconic arrays.

The giant sex chromosome we describe here provides one study system to better to understand alternative trajectories in sex chromosome evolution.

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In the O. Much of the sequence that was unanchored in the O. These two new genome assemblies represent large advances in tilapia genomics, but they have not yet been used to study the origin of the giant sex chromosome. The O. Using the new O. F ST analysis was used to characterize the genome-wide pattern of divergence between males and females of P.

The fine-scale boundaries of the sex-determining region for each species were determined by examining the of WZ patterned SNPs in a kb sliding window. The P. This recharacterization of the sex-determining region in these sex with giant using the new O.

The Japanese medaka Oryzias latipes provides the most suitable outgroup for studying synteny of LG3 in the Oreochromini since medaka has a typical teleost karyotype of 24 chromosome pairs and is the most closely related species with high-quality chromosome-scale assemblies Ichikawa et al.

Due to the fact that the LG3 giant sex chromosome is highly repetitive and contains many gene duplications Ferreira et al.

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Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences.
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