scholarly journals Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

2021 ◽  
Author(s):  
Hannah Munby ◽  
Tyler Linderoth ◽  
Bettina Fischer ◽  
Mingliu Du ◽  
Grégoire Vernaz ◽  
...  
Keyword(s):  
Sex Determination ◽  
Tandem Duplication ◽  
Crater Lake ◽  
Genetic Interactions ◽  
Full Genome ◽  
Genome Data ◽  
Haplochromine Cichlid ◽  
The Face ◽  
Genetic Mechanisms ◽  
Entire Gene

African cichlid fishes not only exhibit remarkably high rates of speciation but also have some of the fastest evolving sex determination systems in vertebrates. However, little is known empirically in cichlids about the genetic mechanisms generating new sex-determining variants, what forces dictate their fate, the demographic scales at which they evolve, and whether they are related to speciation. To address these questions, we looked for sex-associated loci in full genome data from 647 individuals of Astatotilapia calliptera from Lake Masoko, a small isolated crater lake in Tanzania, which contains two distinct ecomorphs of the species. We identified three separate XY systems on recombining chromosomes. Two Y alleles derive from mutations that increase expression of the gonadal soma-derived factor gene (gsdf) on chromosome 7; the first is a tandem duplication of the entire gene observed throughout much of the Lake Malawi haplochromine cichlid radiation to which A. calliptera belongs, and the second is a 5 kb insertion directly upstream of gsdf. Both the latter variant and another 700 bp insertion on chromosome 19 responsible for the third Y allele arose from transposable element insertions. Males belonging to the Masoko deep-water benthic ecomorph are determined exclusively by the gsdf duplication, whereas all three Y alleles are used in the Masoko littoral ecomorph, in which they appear to act antagonistically among males with different amounts of benthic admixture. This antagonism in the face of ongoing admixture may be important for sustaining multifactorial sex determination in Lake Masoko. In addition to identifying the molecular basis of three coexisting sex determining alleles, these results demonstrate that genetic interactions between Y alleles and genetic background can potentially affect fitness and adaptive evolution.

scholarly journals halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Ksenia Krasheninnikova ◽  
Mark Diekhans ◽  
Joel Armstrong ◽  
Aleksei Dievskii ◽  
Benedict Paten ◽  
...  
Keyword(s):  
Large Scale ◽  
Pairwise Alignment ◽  
Synteny Block ◽  
Rapid Identification ◽  
Full Genome Sequence ◽  
Whole Genome ◽  
Full Genome ◽  
Genome Data ◽  
Multiple Alignments ◽  
Binary Format

Abstract Background Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production. Findings halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred–way, reference-free vertebrate alignments built with the Cactus system. Conclusions halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.

scholarly journals Understanding specialism when the jack of all trades can be the master of all

2012 ◽  
Vol 279 (1749) ◽  
pp. 4861-4869 ◽  
Author(s):  
Susanna Remold
Keyword(s):  
Habitat Use ◽  
Recent Work ◽  
Habitat Change ◽  
Directional Selection ◽  
Antagonistic Pleiotropy ◽  
Disease Emergence ◽  
Evolutionary Genetic ◽  
The Face ◽  
Genetic Mechanisms ◽  
Selection For

Specialism is widespread in nature, generating and maintaining diversity, but recent work has demonstrated that generalists can be equally fit as specialists in some shared environments. This no-cost generalism challenges the maxim that ‘the jack of all trades is the master of none’, and requires evolutionary genetic mechanisms explaining the existence of specialism and no-cost generalism, and the persistence of specialism in the face of selection for generalism. Examining three well-described mechanisms with respect to epistasis and pleiotropy indicates that sign (or antagonistic) pleiotropy without epistasis cannot explain no-cost generalism and that magnitude pleiotropy without epistasis (including directional selection and mutation accumulation) cannot explain the persistence of specialism. However, pleiotropy with epistasis can explain all. Furthermore, epistatic pleiotropy may allow past habitat use to influence future use of novel environments, thereby affecting disease emergence and populations' responses to habitat change.

scholarly journals Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shota Yamashita ◽  
Kayoko Yamamoto ◽  
Ryo Matsuzaki ◽  
Shigekatsu Suzuki ◽  
Haruyo Yamaguchi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Convergent Evolution ◽  
Tandem Duplication ◽  
De Novo ◽  
Molecular Genetic ◽  
Somatic Cells ◽  
Whole Genome Sequence ◽  
Rna Seq ◽  
Genome Data ◽  
Genes Encoding

AbstractGerm-soma differentiation evolved independently in many eukaryotic lineages and contributed to complex multicellular organizations. However, the molecular genetic bases of such convergent evolution remain unresolved. Two multicellular volvocine green algae, Volvox and Astrephomene, exhibit convergent evolution of germ-soma differentiation. The complete genome sequence is now available for Volvox, while genome information is scarce for Astrephomene. Here, we generated the de novo whole genome sequence of Astrephomene gubernaculifera and conducted RNA-seq analysis of isolated somatic and reproductive cells. In Volvox, tandem duplication and neofunctionalization of the ancestral transcription factor gene (RLS1/rlsD) might have led to the evolution of regA, the master regulator for Volvox germ-soma differentiation. However, our genome data demonstrated that Astrephomene has not undergone tandem duplication of the RLS1/rlsD homolog or acquisition of a regA-like gene. Our RNA-seq analysis revealed the downregulation of photosynthetic and anabolic gene expression in Astrephomene somatic cells, as in Volvox. Among genes with high expression in somatic cells of Astrephomene, we identified three genes encoding putative transcription factors, which may regulate somatic cell differentiation. Thus, the convergent evolution of germ-soma differentiation in the volvocine algae may have occurred by the acquisition of different regulatory circuits that generate a similar division of labor.

scholarly journals Rice Epigenetic Pathways: Great Genetic Variation and Implication for Rapid Rice Breeding

2018 ◽  
Vol 1 (1) ◽  
pp. 40-46
Author(s):  
Yuan Li ◽  
Erik Persson ◽  
Erik Persson
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
Epigenetic Modification ◽  
Rice Genome ◽  
Rice Breeding ◽  
Genetic Changes ◽  
Genome Data ◽  
Epigenetic Marker ◽  
The Face ◽  
Tremendous Importance

Rice, as one of the most important crops in the world, is facing an ever-accelerating challenge from climate change. Epigenetic modification with its substantially high epimutation rate and the possibility for some epigenetic variation to act as a heritable contributor to crop environmental adaptability may hold great potentials for rapid crop breeding. Epigenetic modification is controlled by epigenetic pathways, and mutations disturbing the epigenetic pathways may lead to significant epigenetic and/or genetic changes. This is especially true for rice, whose genome is rich in epigenetic modifications and transposable elements (TEs) that are generally epigenetically silenced. Here, in this paper, we first reviewed the pathways that establish, maintain and remove rice DNA methylation, which is the most well studied epigenetic marker, as well as the genes that are involved. We then discussed how TEs amplify the phenotypic impact of epigenetic changes that could be a result of epigenetic pathway disturbances. At last, we presented the enormous amount of rice genome data that are publically available, within which great genetic variation in the genes that are involved within the epigenetic pathways is embedded. This genetic variation awaits to be exploited for their potentials in generating a heritable source of variation for rapid environmental adaptation, which may hold tremendous importance for rice breeding in the face of climate change.

scholarly journals Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12390
Author(s):  
Yaqun Zhang ◽  
Chuantao Zhang ◽  
Na Yao ◽  
Jingxian Huang ◽  
Xiangshan Sun ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Molecular Mechanisms ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Penaeus Japonicus ◽  
Genetic Mechanisms

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Genetic and molecular analysis of the autosomal component of the primary sex determination signal of Drosophila melanogaster.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1451-1471 ◽  
Author(s):  
D A Barbash ◽  
T W Cline
Keyword(s):  
Drosophila Melanogaster ◽  
Sex Determination ◽  
Time Course ◽  
Loss Of Function ◽  
Lethal Effects ◽  
Genome Wide ◽  
The Face ◽  
Individual Contributions ◽  
Female Specific ◽  
Inappropriate Expression

Abstract Drosophila sex is determined by the action of the X:A chromosome balance on transcription of Sex-lethal (Sxl), a feminizing switch gene. We obtained loss-of-function mutations in denominator elements of the X:A signal by selecting for dominant suppressors of a female-specific lethal mutation in the numerator element, sisterlessA (sisA). Ten suppressors were recovered in this extensive genome-wide selection. All were mutations in deadpan (dpn), a pleiotropic locus previously discovered to be a denominator element. Detailed genetic and molecular characterization is presented of this diverse set of new dpn alleles including their effects on Sxl. Although selected only for impairment of sex-specific functions, all were also impaired in nonsex-specific functions. Male-lethal effects were anticipated for mutations in a major denominator element, but we found that viability of males lacking dpn function was reduced no more than 50% relative to their dpn- sisters. Moreover, loss of dpn activity in males caused only a modest derepression of the Sxl "establishment" promoter (Sxlpe), the X:A target. By itself, dpn cannot account for the masculinizing effect of increased autosomal ploidy, the effect that gave rise to the concept of the X:A ratio; nevertheless, if there are other denominator elements, our results suggest that their individual contributions to the sex-determination signal are even less than that of dpn. The time course of expression of dpn and of Sxl in dpn mutant backgrounds suggests that dpn is required for sex determination only during the later stages of X:A signaling in males to prevent inappropriate expression of Sxlpe in the face of increasing sis gene product levels.

Is sex determination in germ line and soma controlled by separate genetic mechanisms?

Nature ◽  
1978 ◽  
Vol 272 (5650) ◽  
pp. 249-251 ◽  
Author(s):  
J. L. MARSH ◽  
E. WIESCHAUS
Keyword(s):  
Sex Determination ◽  
Germ Line ◽  
Genetic Mechanisms
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