Reproductive Strategies and Population Genetic Structure in Two Dryland River Floodplain Plants, Marsilea drummondii and Eleocharis acuta

Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems, life history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies that allow plants to persist. Using two aquatic plants, Marsilea drummondii and Eleocharis acuta, we investigated the proportions of sexual and asexual reproduction and self-fertilisation by employing next-generation sequencing approaches, and we used this information to understand the population genetic structure of a large inland floodplain in western New South Wales (NSW), Australia. Asexual vegetative reproduction and self-fertilisation were more common in M. drummondii, but both species used sexual reproduction as the main mode of reproduction. This resulted in a highly differentiated genetic structure between wetlands and a similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species, highlighting the influence of the floodplain landscape and hydrology on structuring population genetic structure. The high levels of genetic variation among wetlands and the low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for the population maintenance of plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment, and reproduction in dryland regions

Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about mechanisms of sex chromosome turnover. Recent studies have made significant progress in better understanding diversity and conservation of reptile sex chromosomes, with however no reptile master sex determination genes identified. Here we describe an integrated genomics and cytogenetics pipeline, combining probes generated from the microdissected sex chromosomes with transcriptome and genome sequencing to explore the sex chromosome diversity in non-model Australian reptiles. We tested our pipeline on a turtle, two species of geckos, and a monitor lizard. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and microchromosomes. We discuss the evolutionary drivers of the slow differentiation and turnover of reptile sex chromosomes

Balanced chromosomal rearrangements associated with hypoprolificacy in australian boars (Sus scrofa domesticus)

Balanced chromosomal rearrangements, mainly reciprocal translocations, are considered to be the causative agent of several clinical conditions in farmed pigs, resulting in hypoprolificacy and economic losses. Literature suggests that reciprocal translocations are heritable and can occur de novo. The prevalence rate of these balanced structural rearrangements of chromosomes differs from country to country and varies between 0.5% and 3.3%. The Australian pig population is descendent of a small founder population and has since been a closed genetic group since the 1980s. Hence, any incident of reciprocal translocation along with the pedigree of boars that contribute sperm for artificial insemination has the potential to have an economic consequence. To date, there has been no published account for screening of reciprocal translocation associated with hypoprolificacy in the Australian pig population. In this study, we performed standard and molecular cytogenetic analyses to identify evidence of chromosome rearrangements and their association with hypoprolificacy in a representative 94 boar samples from a commercial nucleus herd. We identified three novel rearrangements between chromosomes 5 and 14, between chromosomes 9 and 10, and between chromosomes 10 and 12. In addition, we also detected a reciprocal translocation between chromosomes 3 and 16 that has previously been detected in pig herds in France. The prevalence rate was 6.38% within the samples used in this study. All four rearrangements were found to have an association with hypoprolificacy. Further study and routine monitoring will be necessary to identify any further rearrangements that will allow breeders to prevent the propagation of reciprocal translocations from generation to generation within the Australian pig population

W Chromosome Evolution by Repeated Recycling in the Frog <i>Glandirana rugosa</i>

The Y or W sex chromosome of a heteromorphic pair is usually heterochromatinised and degenerated. However, whether chromosome degeneration constantly proceeds toward an extreme end is not fully understood. Here, we present a case of intermittent evolution of W chromosomes caused by interpopulation hybridisation in the Japanese soil-frog, Glandirana rugosa. This species includes two heteromorphic sex chromosome systems, which are separated into geographic populations, namely the XY and ZW groups. In this study, to uncover the evolutionary mechanisms of the heterogeneous W chromosomes, we genetically investigated the geographic differentiation of the ZW populations along with the closely located XY populations. Analysis of mitochondrial cytochrome b sequences detected three distinct clades, named ZW1, ZW2, and ZW3. High throughput analyses of nuclear genomic DNA showed that autosomal alleles of XY populations were deeply introgressed into the ZW3 sub-group. Based on the genotypes of sex-linked single nucleotide polymorphisms, W-borne androgen receptor gene expression, and WW developmental mortality, we concluded that the X chromosomes were recycled to W chromosomes. Upon inclusion of two cases from another group, Neo-ZW, we observed that the X chromosomes were recycled independently at least four times to the new W chromosomes: a repetition of degeneration and resurrection

Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua

Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1-0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable

Differences in homomorphic sex chromosomes are associated with population divergence in sex determination in carinascincus ocellatus (Scincidae:Lygosominae)

Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (&lt;1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution

Sex-linked markers in an Australian frog Platyplectrum ornatum (Limnodynastidae) with a small genome and homomorphic sex chromosomes

Abstract Amphibians have highly diverse sex-determining modes leading to a notable interest in vertebrate sex determination and sex chromosome evolution. The identification of sex-determining systems in amphibians, however, is often difficult as a vast majority consist of homomorphic sex chromosomes making them hard to distinguish. In this study, we used Diversity Array Technology sequencing (DArTseq) to identify the sex-determining system in the ornate burrowing frog from Australia, Platyplectrum ornatum. We applied DArTseq to 44 individuals, 19 males and 25 females, collected from two locations to develop sex-linked markers. Unexpectedly, these 44 individuals were classified into two distinct population clusters based on our SNP analyses, 36 individuals in cluster 1, and 8 individuals in cluster 2. We then performed sex-linkage analyses separately in each cluster. We identified 35 sex-linked markers from cluster 1, which were all associated with maleness. Therefore, P. ornatum cluster 1 is utilising a male heterogametic (XX/XY) sex-determining system. On the other hand, we identified 210 sex-linked markers from cluster 2, of which 89 were male specific, i.e., identifying XX/XY sex determining system and 111 were female specific, i.e., identifying ZZ/ZW sex determining system, suggesting existence of either male or female heterogametic sex determining system in cluster 2. We also performed cytogenetic analyses in 1 male and 1 female from cluster 1; however, we did not detect any visible differentiation between the X and Y sex chromosomes. We also mapped sex-linked markers from the two clusters against the P. ornatum genome and our comparative analysis indicated that the sex chromosomes in both clusters shared homologies to chromosome 10 (autosome) of Rana temporaria and ZWY sex chromosome of Xenopus tropicalis. Our preliminary data suggest that it is plausible that the cluster 2 has a potential to be either male or female heterogamety in sex determination, requiring further investigation