Distribution and amplification of interstitial telomeric sequences (ITSs) in Australian dragon lizards support frequent chromosome fusions in Iguania

Telomeric sequences are generally located at the ends of chromosomes; however, they can also be found in non-terminal chromosomal regions when they are known as interstitial telomeric sequences (ITSs). Distribution of ITSs across closely related and divergent species elucidates karyotype evolution and speciation as ITSs provide evolutionary evidence for chromosome fusion. In this study, we performed physical mapping of telomeric repeats by fluorescence in situ hybridisation (FISH) in seven Australian dragon lizards thought to represent derived karyotypes of squamate reptiles and a gecko lizard with considerably different karyotypic feature. Telomeric repeats were present at both ends of all chromosomes in all species, while varying numbers of ITSs were also found on microchromosomes and in pericentromeric or centromeric regions on macrochromosomes in five lizard species examined. This suggests that chromosomal rearrangements from ancestral squamate reptiles to Iguania occurred mainly by fusion between ancestral types of acrocentric chromosomes and/or between microchromosomes, leading to appearance of bi-armed macrochromosomes, and in the reduction of microchromosome numbers. These results support the previously proposed hypothesis of karyotype evolution in squamate reptiles. In addition, we observed the presence of telomeric sequences in the similar regions to heterochromatin of the W microchromosome in Pogona barbata and Doporiphora nobbi, while sex chromosomes for the two species contained part of the nucleolar organiser regions (NORs). This likely implies that these ITSs are a part of the satellite DNA and not relics of chromosome fusions. Amplification of telomeric repeats may have involved heterochromatinisation of sex-specific W chromosomes and play a role in the organisation of the nucleolus

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

We report here the first genome assembly and annotation of the human-pathogenic fungus Scedosporium aurantiacum, with a predicted 10,525 genes, and 11,661 transcripts. The strain WM 09.24 was isolated from the environment at Circular Quay, Sydney, New South Wales, Australi

Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1

Background: Scant genomic information from non-avian reptile sex chromosomes is available, and for only a few lizards, several snakes and one turtle species, and it represents only a small fraction of the total sex chromosome sequences in these species. Results: We report a 352 kb of contiguous sequence from the sex chromosome of a squamate reptile, Pogona vitticeps, with a ZZ/ZW sex microchromosome system. This contig contains five protein coding genes (oprd1, rcc1, znf91, znf131, znf180), and major families of repetitive sequences with a high number of copies of LTR and non-LTR retrotransposons, including the CR1 and Bov-B LINEs. The two genes, oprd1 and rcc1 are part of a homologous syntenic block, which is conserved among amniotes. While oprd1 and rcc1 have no known function in sex determination or differentiation in amniotes, this homologous syntenic block in mammals and chicken also contains R-spondin 1 (rspo1), the ovarian differentiating gene in mammals. In order to explore the probability that rspo1 is sex determining in dragon lizards, genomic BAC and cDNA clones were mapped using fluorescence in situ hybridisation. Their location on an autosomal microchromosome pair, not on the ZW sex microchromosomes, eliminates rspo1 as a candidate sex determining gene in P. vitticeps. Conclusion: Our study has characterized the largest contiguous stretch of physically mapped sex chromosome sequence (352 kb) from a ZZ/ZW lizard species. Although this region represents only a small fraction of the sex chromosomes of P. vitticeps, it has revealed several features typically associated with sex chromosomes including the accumulation of large blocks of repetitive sequences

4.脳腫瘍患者における頭蓋内圧の日内変動に関する研究 : とくにA波について(昭和55年度猪之鼻奨学会研究補助金報告)

BACKGROUND Squamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it difficult to reconstruct the events that have led to extant squamate karyotypic diversity. The purpose of this study was to anchor the recently sequenced central bearded dragon (Pogona vitticeps) genome to chromosomes to trace the evolution of squamate chromosomes. Assigning sequence to sex chromosomes was of particular interest for identifying candidate sex determining genes. RESULTS By using two different approaches to map conserved blocks of genes, we were able to anchor approximately 42 % of the dragon genome sequence to chromosomes. We constructed detailed comparative maps between dragon, anole and chicken genomes, and where possible, made broader comparisons across Squamata using cytogenetic mapping information for five other species. We show that squamate macrochromosomes are relatively well conserved between species, supporting findings from previous molecular cytogenetic studies. Macrochromosome diversity between members of the Toxicofera clade has been generated by intrachromosomal, and a small number of interchromosomal, rearrangements. We reconstructed the ancestral squamate macrochromosomes by drawing upon comparative cytogenetic mapping data from seven squamate species and propose the events leading to the arrangements observed in representative species. In addition, we assigned over 8 Mbp of sequence containing 219 genes to the Z chromosome, providing a list of genes to begin testing as candidate sex determining genes. CONCLUSIONS Anchoring of the dragon genome has provided substantial insight into the evolution of squamate genomes, enabling us to reconstruct ancestral macrochromosome arrangements at key positions in the squamate phylogeny, demonstrating that fusions between macrochromosomes or fusions of macrochromosomes and microchromosomes, have played an important role during the evolution of squamate genomes. Assigning sequence to the sex chromosomes has identified NR5A1 as a promising candidate sex determining gene in the dragon.This project was funded by ARC DP110104377, a Faculty of Applied Science postdoctoral fellowship to DO’M and University of Canberra strategic funds awarded to AG and JED

The interplay between Heterochromatin Protein (HP1) and histone variant H2A.Z in gene expression regulation

It is now clearly established that the central regulator of eukaryotic gene transcription is the organization of the genome into chromatin. Chromatin performs this crucial function by partitioning the genome into functionally specialised domains and subdomains, that is heterochromatin and euchromatin. Chromatin is built from nucleosomes, the universal repeating protein-DNA complex in all eukaryotic cells. Underpinning the proper regulation of gene expression are epigenetic-based mechanisms that regulate the structure of chromatin. These include histone modifications, the incorporation of histone variants and the binding of architectural chromatin proteins (ACPs). ACPs are universal nuclear proteins that utilise the structural properties of chromatin to create functionally unique higher-order chromatin structures. The most intensively studied ACP is HP1. HP1 is a highly conserved and essential silencing protein. Mammalian HP1 exists in three isoforms; HP1a, HP1b, and HP1g. It is still unknown why these three different isoforms exist? In thesis, I examined whether HP1a and HP1b have unique or overlapping functions in determining the phenotype of a cell and in regulating gene expression. The different HP1 isoforms have received considerable attention recently because they are aberrantly expressed in cancers. However, their role is controversial because in some cancers the expression of certain isoforms increases and in other types of cancers, it decreases. Further, how they contribute to cancer is unclear. In this thesis, I investigated whether altering the expression of HP1a or HP1b is sufficient to drive the major phenotypic changes associated with malignancy and also examined the associated changes in gene expression. Chromatin is a complex structure comprised of a multitude of different biochemical components. Therefore, no individual component of chromatin works in isolation and its function can be modulated by other components of chromatin. One important way the structure and function of chromatin is regulated is by the replacement of the major histones with their variant forms. Significant to the function of HP1 is the essential histone variant H2A.Z. Results from the Tremethick laboratory have revealed that HP1a is a reader of H2A.Z and moreover, they cooperate to form compacted chromatin structures. Finally, I investigated the interplay between H2A.Z and HP1 on regulating gene expression and changes to cellular morphology and function. To address these aims, isogenic MCF10A (non-invasive) and MCF10Ca1a (invasive) human breast epithelial cell lines were employed. Specifically, I established single and double MCF10A knockdown cell lines and compared the associated phenotypic changes with the malignant MCF10Ca1a cell line. In addition, I performed RNA and ChIP-seq experiments to study the impact of these knockdowns of HP1 and/or H2A.Z on gene expression. The major conclusions of this thesis: 1) the knockdown of HP1a and HP1b had different effects on cellular proliferation and cell migration indicating that they have different cellular functions; 2) neither the single nor double knockdown of HP1a and HP1b induced a MCF10Ca1a malignant-like phenotype. However, the combined knockdown produced an interesting cellular change, in which these shHP1a and shHP1b cells stopped dividing and entered the G0-G1 stage of the cell cycle. 3) most interestingly, the combined depletion of HP1a and HP1b showed that a large number of misregulated genes were involved in important centromere organisation and functions; 4) while RNA-seq data indicated that loss of HP1a can be compensated by HP1b and vice versa, unexpectedly the ChIP-seq data revealed that this was not the case suggesting that proper gene regulation can be maintained by sub optimal amounts of HP1a or HP1b; and 6) H2A.Z was required for the recruitment of HP1a and HP1b on the gene bodies of inactive and active genes, as well as on centromeric DNA repeat elements

Amplification of microsatellite repeat motifs is associated with the evolutionary differentiation and heterochromatinization of sex chromosomes in Sauropsida

The sex chromosomes in Sauropsida (reptiles and birds) have evolved independently many times. They show astonishing diversity in morphology ranging from cryptic to highly differentiated sex chromosomes with male (XX/XY) and female heterogamety (ZZ/ZW). Comparing such diverse sex chromosome systems thus provides unparalleled opportunities to capture evolution of morphologically differentiated sex chromosomes in action. Here, we describe chromosomal mapping of 18 microsatellite repeat motifs in eight species of Sauropsida. More than two microsatellite repeat motifs were amplified on the sex-specific chromosome, W or Y, in five species (Bassiana duperreyi, Aprasia parapulchella, Notechis scutatus, Chelodina longicollis, and Gallus gallus) of which the sex-specific chromosomes were heteromorphic and heterochromatic. Motifs (AAGG)n and (ATCC)n were amplified on the W chromosome of Pogona vitticeps and the Y chromosome of Emydura macquarii, respectively. By contrast, no motifs were amplified on the W chromosome of Christinus marmoratus, which is not much differentiated from the Z chromosome. Taken together with previously published studies, our results suggest that the amplification of microsatellite repeats is tightly associated with the differentiation and heterochromatinization of sex-specific chromosomes in sauropsids as well as in other taxa. Although some motifs were common between the sex-specific chromosomes of multiple species, no correlation was observed between this commonality and the species phylogeny. Furthermore, comparative analysis of sex chromosome homology and chromosomal distribution of microsatellite repeats between two closely related chelid turtles, C. longicollis and E. macquarii, identified different ancestry and differentiation history. These suggest multiple evolutions of sex chromosomes in the Sauropsida

Additional file 6: of Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

Script A1 to scan the synteny files to interim super-scaffolds for P. vitticeps. (CGI 22 kb

Proceedings of International Web Conference in Civil Engineering for a Sustainable Planet

This proceeding contains articles of the various research ideas of the academic community and practitioners accepted at the "International Web Conference in Civil Engineering for a Sustainable Planet (ICCESP 2021)". ICCESP 2021 is being Organized by the Habilete Learning Solutions, Kollam in Collaboration with American Society of Civil Engineers (ASCE), TKM College of Engineering, Kollam, and Baselios Mathews II College of Engineering, Kollam, Kerala, India. Conference Title: International Web Conference in Civil Engineering for a Sustainable PlanetConference Acronym: ICCESP 2021Conference Date: 05–06 March 2021Conference Location: Online (Virtual Mode)Conference Organizer: Habilete Learning Solutions, Kollam, Kerala, IndiaCollaborators: American Society of Civil Engineers (ASCE), TKM College of Engineering, Kollam, and Baselios Mathews II College of Engineering, Kollam, Kerala, India