Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes.

Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.

Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an "ancestral amniote super-sex chromosome"?

Sex chromosomes in some amniotes share linkage homologies with distantly related taxa in regions orthologous to squamate reptile chromosome 2 (SR2) and the snake W sex chromosome. Thus, the SR2 and W chromosomes may formerly have been part of a larger ancestral amniote super-sex chromosome. Comparison of various sex chromosomal linkage homologies in Toxicofera with those in other amniotes offers an excellent model to assess key cytological differences, to understand the mechanisms of amniote sex chromosome evolution in each lineage and the existence of an ancestral amniote super-sex chromosome. Chromosome maps of four species of Toxicofera were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Different macrochromosome linkage homologies were highly conserved among Toxicofera, and at least two BACs (CH261-125F1 and CH261-40D6) showed partial homology with sex chromosomes of amniotes associated with SR2, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial linkage homologies. The present data also suggest a possible multiple fission mechanism of an ancestral super-sex chromosome, which resulted in further development of various sex chromosomal linkages of Toxicofera based on particular properties that favored the role of sex chromosomes.

Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements.

Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species.

Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution?

BACKGROUND: Unlike the chromosome constitution of most snakes (2n=36), the cobra karyotype shows a diploid chromosome number of 38 with a highly heterochromatic W chromosome and a large morphologically different chromosome 2. To investigate the process of sex chromosome differentiation and evolution between cobras, most snakes, and other amniotes, we constructed a chromosome map of the Siamese cobra (Naja kaouthia) with 43 bacterial artificial chromosomes (BACs) derived from the chicken and zebra finch libraries using the fluorescence in situ hybridization (FISH) technique, and compared it with those of the chicken, the zebra finch, and other amniotes. RESULTS: We produced a detailed chromosome map of the Siamese cobra genome, focusing on chromosome 2 and sex chromosomes. Synteny of the Siamese cobra chromosome 2 (NKA2) and NKAZ were highly conserved among snakes and other squamate reptiles, except for intrachromosomal rearrangements occurring in NKA2. Interestingly, twelve BACs that had partial homology with sex chromosomes of several amniotes were mapped on the heterochromatic NKAW as hybridization signals such as repeat sequences. Sequence analysis showed that most of these BACs contained high proportions of transposable elements. In addition, hybridization signals of telomeric repeat (TTAGGG)n and six microsatellite repeat motifs ((AAGG)8, (AGAT)8, (AAAC)8, (ACAG)8, (AATC)8, and (AAAAT)6) were observed on NKAW, and most of these were also found on other amniote sex chromosomes. CONCLUSIONS: The frequent amplification of repeats might involve heterochromatinization and promote sex chromosome differentiation in the Siamese cobra W sex chromosome. Repeat sequences are also shared among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial syntenies. Alternatively, amplification of microsatellite repeat motifs could have occurred independently in each lineage, representing convergent sex chromosomal differentiation among amniote sex chromosomes.

Assessing developmental and transcriptional effects of PM2.5 on zebrafish embryos.

Investigating fine particulate matter (PM2.5) toxicity is crucial for health risk assessment and pollution control. This study explores the developmental toxicity of two PM2.5 sources: standard reference material 2786 (NIST, USA) and PM2.5 from Chakri Naruebodindra Medical Institute (CNMI, Thailand) located in the Bangkok Metropolitan area. Zebrafish embryos exposed to these samples exhibited embryonic mortality, with 50% lethal concentration (LC50) values of 1476 µg/mL for standard PM2.5 and 512 µg/mL for CNMI PM2.5. Morphological analysis revealed malformations, including pericardial and yolk sac edema, and blood clotting in both groups. Gene expression analysis highlighted source-specific effects. Standard PM2.5 downregulated sod1 and cat while upregulating gstp2. Inflammatory genes tnf-α and il-1b were upregulated, and nfkbi-αa was downregulated. Apoptosis-related genes bax, bcl-2, and casp3a were downregulated. CNMI PM2.5 consistently downregulated all examined genes. These findings underscore PM2.5 source variability's significance in biological system impact assessment, providing insights into pollutant-gene expression interactions. The study emphasizes the need for source-specific risk assessment and interventions to address PM2.5 exposure's health impacts effectively.

Effects of polystyrene nanoplastic size on zebrafish embryo development.

Polystyrene nanoplastics (PS) require a comprehensive evaluation of their toxicity and potential risks to humans and the environment. The zebrafish model, a well-established animal model increasingly utilized for nanotoxicity assessments, was employed in this study. Our research aimed to explore the toxic effects of PS with sizes of 30, 100, 200, and 450 nm on zebrafish embryos. Exposure experiments were conducted on embryos at 4 h post-fertilization (hpf) using various concentrations of nanoparticles (20, 40, 60, 80, and 100 mg/L) until 96 hpf. Notably, PS ranging from 100 to 450 nm did not adversely affect zebrafish embryo development. However, PS with a size of 30 nm at a concentration of 100 mg/L resulted in embryo mortality but not embryonic malformations. Furthermore, our investigation confirmed the uptake of these nanoparticles by zebrafish larvae following the opening of their mouths, with the particles being found predominantly in the digestive system of the larvae. Additionally, 30 nm PS were found to significantly modulate the expression levels of genes associated with oxidative stress and apoptosis. These findings highlight the developmental impacts of 30 nm PS on zebrafish embryos, raising concerns about potential similar consequences in humans. Considering our findings, it is essential to encourage further research into the management and regulation of PS to mitigate their potential environmental and health impacts.

Impact of a real food matrix and in vitro digestion on properties and acute toxicity of polystyrene microparticles.

Although it is proved that humans ingest microplastics via food, and microplastics were found in human tissues, blood and feces, there needs to be more data on the properties and health-related effects of plastic particles that interact with food and undergo digestion. This study aimed to examine the impact of a real food matrix, milk, on the behavior and gastrointestinal fate of polystyrene microparticles (PSMP). In the presence of the food matrix, the net negative ζ-potential values of PSMP (diameter size of 1.823 µm) decreased significantly due to the formation of the corona, mostly consisting of α and ß-casein fragments. Protein corona profiles and morphologies of particles incubated with whole and skim milk were found to be similar, and the protein profiles were completely altered after in vitro digestion simulation. In vitro and in vivo toxicity studies showed that neither bare PSMP nor food-interacted PSMP pose acute toxicity on the Caco-2 cell line and zebrafish embryos under the chosen experimental conditions. In summary, these results may contribute to a better understanding of changes that microplastics undergo in foods. Further studies on repeated exposure or chronic toxicity are needed to fully reveal the effect of food matrix on microplastic toxicity.

Development of Biomaterials Based on Biomimetic Trace Elements Co-Doped Hydroxyapatite: Physical, In Vitro Osteoblast-like Cell Growth and In Vivo Cytotoxicity in Zebrafish Studies.

Synthesized hydroxyapatite (sHA)-calcium phosphate (CaP) based biomaterials play a vital role and have been widely used in the process of bone regeneration for bone defect repair, due to their similarities to the inorganic components of human bones. However, for bone tissue engineering purpose, the composite components, physical and biological properties, efficacy and safety of sHA still need further improvements. In this work, we synthesized inhomogeneous hydroxyapatite based on biomimetic trace elements (Mg, Fe, Zn, Mn, Cu, Ni, Mo, Sr, Co, BO33-, and CO32-) co-doped into HA (THA) (Ca10-δMδ(PO4)5.5(CO3)0.5(OH)2, M = trace elements) via co-precipitation from an ionic solution. The physical properties, their bioactivities using in vitro osteoblast cells, and in vivo cytotoxicity using zebrafish were studied. By introducing biomimetic trace elements, the as-prepared THA samples showed nanorod (needle-like) structures, having a positively charged surface (6.49 meV), and showing paramagnetic behavior. The bioactivity studies demonstrated that the THA substrate can induce apatite particles to cover its surface and be in contact with surrounding simulated body fluid (SBF). In vitro biological assays revealed that the osteoblast-like UMR-106 cells were well-attached with growth and proliferation on the substrate's surface. Upon differentiation, enhanced ALP (alkaline phosphatase) activity was observed for bone cells on the surface of the THA compared with that on the control substrates (sHA). The in vivo performance in embryonic zebrafish studies showed that the synthesized THA particles are nontoxic based on the measurements of essential parameters such as survivability, hatching rate, and the morphology of the embryo. The mechanism of the ions release profile using digital conductivity measurement revealed that sustained controlled release was successfully achieved. These preliminary results indicated that the synthesized THA could be a promising material for potential practical applications in bone tissue engineering.

Investigation on the physical properties and biocompatibility of zirconia-alumina-silicate@diopside composite materials and its in vivo toxicity study in embryonic zebrafish.

Bioceramic materials have a wide range of applications in the biomedical field, such as in the repair of bone defects and dental surgery. Silicate-based bioceramics have attracted biomedical researchers' interest due to their bioactivity and biodegradability. In this study, extended the scope of ZAS utilization in bone tissue engineering by introducing calcium-magnesium-silicate (diopside, CMS) as an interface material aim to develop a machinable bioceramic composite (ZASCMS) by the sol-gel method. The physicochemical characterization, in vitro biological properties and in vivo zebrafish cytotoxicity study of ZAS-based composites as a function of CMS contents, 0, 25, 50, 75 and 100 wt%, were performed. Results showed that the as-prepared ZASCMS possessed porous architecture with well-interconnected pore structure. Results also revealed that the mechanical properties of ZASCMS composite materials were gradually improved with increasing CMS contents. The ZASCMS composites with more than 50 wt% CMS had the highest compressive strength and modulus of 6.78 ± 0.62 MPa and 340.10 ± 16.81 MPa, respectively. Regarding in vitro bioactivities, the composite scaffolds were found to stimulate osteoblast-like UMR-106 cell adhesion, growth, and proliferation. The antibacterial activity of the ZASCMS composite scaffolds was tested against Staphylococcus epidermidis (S. epidermidis) and Escherichia coli (E. coli) also exhibited an antibacterial property. Furthermore, the in vivo studies using embryonic zebrafish were exposed to as-prepared particles (0-500 µg mL-1) and showed that the synthesized ZAS, CMS and ZASCMS composite particles were non-toxic based on the evaluation of survivability, hatching rate and embryonic morphology. In conclusions, our results indicated that the synthesized composite exhibited their biological properties and antibacterial activity, which could well be a promising material with high potential to be applied in orthopaedic and dental tissue engineering.

Developmental effects of sesamolin on zebrafish (Danio rerio) embryos.

Sesamolin is one of the major active compounds found in sesame seeds (Sesamum indicum L.) that are commonly and increasingly used as an ingredient in cuisines and various food products. The compound has been reported to have several pharmaceutical activities such as antioxidant, antimicrobial, neuroprotective, and anticancer. However, the toxicological profile of sesamolin does not currently include developmental toxicity. In this study, we assessed sesamolin toxicity to embryonic development of zebrafish by exposure for 72 h at concentrations ranging from 10 to 50 µM. The evaluation revealed that sesamolin did not affect survival and hatching rates. However, it did induce embryo malformations and reduced embryonic heart rates in a dose-dependent manner. By qRT-PCR analysis, it downregulated the expression of oxidative stress-related genes, including superoxide dismutase 1 (sod1), catalase (cat), and glutathione S-transferase pi 2 (gstp2). Alkaline phosphatase staining of embryos revealed that sesamolin inhibited the development of subintestinal vessels, and hemoglobin staining revealed a negative impact on embryonic erythropoiesis. These findings showed that sesamolin affected genes related to angiogenesis and erythropoiesis. The risks of sesamolin to embryonic development found in this study may imply similar effects in humans and other mammals.

Transparent Anti-SARS COV-2 Film from Copper(I) Oxide Incorporated in Zeolite Nanoparticles.

The high antibacterial and antiviral performance of synthesized copper(I) oxide (Cu2O) incorporated in zeolite nanoparticles (Cu-Z) was determined. Various Cu contents (1-9 wt %) in solutions were loaded in the zeolite matrix under neutral conditions at room temperature. All synthesized Cu-Z nanoparticles showed high selectivity of the cuprous oxide, as confirmed by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis. An advantage of the prepared Cu-Z over the pristine Cu2O nanoparticles was its high thermal stability. The 7 and 9 wt % Cu contents (07Cu-Z and 09Cu-Z) exhibited the best activities to deactivate Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus bacteria. The film coated with 07Cu-Z nanoparticles also had high antiviral activities against porcine coronavirus (porcine epidemic diarrhea virus, PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Specifically, the 07Cu-Z-coated film could reduce 99.93% of PEDV and 99.94% of SARS-CoV-2 viruses in 5 min of contact time, which were higher efficacies and faster than those of any previously reported works. The anti-SARS-CoV-2 virus film was coated on a low-cost PET or PVC film. A very small amount of cuprous oxide in zeolite was used to fabricate the antivirus film; therefore, the film was more transparent (79.4% transparency) than the cuprous oxide film or other commercial products. The toxicity of 07Cu-Z nanoparticles was determined by a toxicity test on zebrafish embryo and a skin irritation test to reconstruct a human epidermis (RhE) model. It was found that the impact on the aquatic environment and human skin was lower than that of the pristine Cu2O.

Fabrication of biocompatible magneto-fluorescence nanoparticles as a platform for fluorescent sensor and magnetic hyperthermia applications.

Multifunctional nanoparticles with special magnetic and optical properties have been attracting a great deal of attention due to their important applications in the bioanalytical and biomedical fields. In this study, we report the fabrication of biocompatible magneto-fluorescence nanoparticles consisting of carbon dots (CDots) and silica-coated cobalt-manganese nanoferrites (Co0.5Mn0.5Fe2O4) (CoMnF@Si@CDots) (MagSiCDots) by a facile hydrothermal method. The as-prepared MagSiCDots have a particle size of 100-120 nm and show a negative zeta potential of -35.50 mV at a neutral pH. The fluorescence spectrum of the MagSiCDots nanoparticles consists of sharp excitation at 365 nm and broad blue light emission with a maximum wavelength of 442.5 nm and the MagSiCDots exhibit superparamagnetic behaviour with a saturation magnetization of 11.6 emu g-1. The potential of MagSiCDots as a fluorescent sensor and be used for magnetic hyperthermia applications. It is seen that the fluorescent intensity of a colloidal solution (a hydrogen sulfide (H2S) solution containing MagSiCDots nanoparticles) has a linear relationship with the H2S concentration range of 0.2-2 µM. The limit of detection (LOD) of H2S by our MagSiCDots particles is 0.26 µM and they remain stable for at least 90 min. To test the suitability of the MagSiCDots nanoparticles for use in hyperthermia application, induction heating using an AMF was done. It was observed that these nanoparticles had a specific absorption rate (SAR) of 28.25 W g-1. The in vitro and in vivo cytotoxicity of MagSiCDots were tested on HeLa cells lines. The results show a cell viability of about 85% when exposed to 100 µg mL-1 concentration of the particles. The in vivo cytotoxicity using zebrafish assay also confirmed the non-toxicity and biocompatibility of the nanoparticles to living cells. The reported data demonstrate that by combining CoMnF@Si and fluorescent CDots into a single system, not only nontoxic multifunctional nanomaterials but also multimodal nanoparticles for several applications, such as hazard gas detection and acting as a biocompatible heat source for therapeutic treatment of cancer, are provided.

Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana (Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes.

The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.

Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes.

Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell's viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action.

Predictive genetic plan for a captive population of the Chinese goral (Naemorhedus griseus) and prescriptive action for ex situ and in situ conservation management in Thailand.

Captive breeding programs for endangered species can increase population numbers for eventual reintroduction to the wild. Captive populations are typically small and isolated, which results in inbreeding and reduction of genetic variability, and may lead to an increased risk of extinction. The Omkoi Wildlife Breeding Center maintains the only Thai captive Chinese goral (Naemorhedus griseus) population, and has plans to reintroduce individuals into natural isolated populations. Genetic variability was assessed within the captive population using microsatellite data. Although no bottleneck was observed, genetic variability was low (allelic richness = 7.091 ± 0.756, He = 0.455 ± 0.219; He < Ho) and 11 microsatellite loci were informative that likely reflect inbreeding. Estimates of small effective population size and limited numbers of founders, combined with wild-born individuals within subpopulations, tend to cause reduction of genetic variability over time in captive programs. This leads to low reproductive fitness and limited ability to adapt to environmental change, thereby increasing the risk of extinction. Management of captive populations as evolutionarily significant units with diverse genetic backgrounds offers an effective strategy for population recovery. Relocation of individuals among subpopulations, or introduction of newly captured wild individuals into the captive program will help to ensure the future security of Chinese goral. Implications for future conservation actions for the species are discussed herein.

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation.

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can "jump" and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10-6% to 5.63 × 10-2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

Dynamics of telomere length in captive Siamese cobra (Naja kaouthia) related to age and sex.

Telomeres comprise tandem repeated DNA sequences that protect the ends of chromosomes from deterioration or fusion with neighboring chromosomes, and their lengths might vary with sex and age. Here, age- and sex-related telomere lengths in male and female captive Siamese cobras (Naja kaouthia) were investigated using quantitative real-time polymerase chain reaction based on cross-sectional data. A negative correlation was shown between telomere length and body size in males but not in females. Age-related sex differences were also recorded. Juvenile female snakes have shorter telomeres relative to males at up to 5 years of age, while body size also rapidly increases during this period. This suggests that an accelerated increase in telomere length of female cobra results from sex hormone stimulation to telomerase activity, reflecting sexually dimorphic phenotypic traits. This might also result from amplification of telomeric repeats on sex chromosomes. By contrast, female Siamese cobras older than 5 years had longer telomeres than males. Diverse sex hormone levels and oxidative stress parameters between sexes may affect telomere length.

Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus).

The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woolly-necked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand.

Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles.

To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194-210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage.

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.