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Background: Bruguiera hainesii C.G. Rogers 1919, a true mangrove tree is a critically endangered species (CR) in Vietnam. This species is restricted to the Con Dao National Park, Ba Ria-Vung Tau province, where it occurs in very tiny populations. However, the exploration of the chloroplast genome of B. hainesii in Vietnam has a serious lack of information. It is extremely challenging to promote the conservation of B. hainesii. Therefore, urgently required to discover and comprehend the chloroplast genome of B. hainesii. Methods: To detect evolutionary analysis between mangroves, we sequenced the complete chloroplast genome of B. hainesii using next-generation sequencing technology (Illumina Hiseq X Ten). Results: We sequenced and assembled the complete chloroplast genome of B. hainesii, which was deposited in GenBank as accession number OR086085. The DNA was circular with 164,305 bp length, comprising 37% GC. The genome contained a large single-copy region of 91,724 bp, inverted repeat regions of 26,360 bp, and a short single-copy region of 19,861 bp. Furthermore, it contained 130 genes, consisting of 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. We detected 131 single-sequence repeats, including 119 mononucleotides, 11 dinucleotides, and one trinucleotide. Phylogenetic analysis showed strong support that B. hainesii was sister to B. cylindrica. Conclusions: The findings in this study provide a foundation for species identification, evolutionary genetics, and the conservation of endangered B. hainesii in Vietnam. [ABSTRACT FROM AUTHOR]

Aquaculture is a promising of the Nile tilapia (Oreochromis niloticus, L.), an important issue in Egypt. The present study's objective was to use short sequence repeats markers (SSRs) in the early sexing of O. niloticus. Molecular markers identification in fish includes SSRs markers that were very useful for investigating sexdetermination system, sex-related genes, and sex chromosomes. The fin-clip tissue of examined fish was used for DNA extraction and the amplification of SSRs and sex determination; twenty primer pairs were tested. The results showed that, from the tested 21 primers of SSRs markers, four primers had significant differences between males and females. It was observed that females were homozygous, and males may be heterozygous or homozygous for the alternative bands. The females were homozygous, males were heterozygous for two SSRs markers, the females were homozygous, and males were homozygous for the alternative alleles for the other two markers. In conclusion, the results of the present study and the previous ones confirm the possibility of using short sequence repeats markers (SSRs) in the sex determination of fish species, including Nile tilapia (Oreochromis niloticus, L.). SSRs markers could be used in the early sexing detection of the Nile tilapia breeding programs and for producing supermale YY without needing progeny test. [ABSTRACT FROM AUTHOR]

How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits—mode of genomic inheritance—influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum , which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S–5.8S–28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA–histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction—with potential functional consequences related to the loss of sexual reproduction. [ABSTRACT FROM AUTHOR]

Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as "noise" in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the "dominant" haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf's law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers. [ABSTRACT FROM AUTHOR]

Many studies have shown that folate deficiency induces DNA hypomethylation and DNA damage. DNA hypomethylation is thought to occur during DNA replication through deficiency of the DNA methylation donor synthesized using folate. However, the relationship between DNA hypomethylation and DNA damage caused by folate deficiency is not well understood. Here, we analyzed DNA damage caused by folate deficiency during the cell cycle S phase in which DNA hypomethylation occurs. Using HeLa cells, we first detected accumulation of intranuclear γ-H2A.X, a DNA double strand break marker, by immunofluorescent staining. We found that DNA damage occurs primarily during S phase, and that folate deficiency enhanced S phase-dependent DNA damage. We also found that folate deficiency caused slowing of the DNA replication fork and a delay in the onset of middle-late S phase. Detailed analyses of DNA damage in S phase progression suggested that the folate deficiency-induced DNA damage increased in all stages of S phase, particularly in middle-late S phase cells. To examine the relationship between DNA damage and DNA hypomethylation, we analyzed the methylation state of the promoter region of the human LINE1 repetitive sequence, where heterochromatin is formed and replicated during middle to late S phase. We found that DNA methylation decreased by about 10% under the folate deficiency condition. Taken together, our results suggest that DNA hypomethylation is associated with DNA damage caused by folate deficiency. [ABSTRACT FROM AUTHOR]

Landscape level species assessments are rarely available to inform conservation planning. Recent advances in multi-taxa survey techniques, however, have made them more obtainable by improving efficiency of collecting species occurrence data and genetic samples. Here, we used a multi-taxa survey technique to provide a landscape level portrait of fisher (Pekania pennanti) population status in a portion of the northern Rockies where the species' history has been heavily influenced by humans. From 2010 to 2014 we deployed 497 winter forest carnivore bait stations across a 23,000 km2 study area centered on northern Idaho, United States. The stations collected remote camera images and hair samples for DNA analysis. We used 12 microsatellite loci to identify 58 individual fisher in the study area. We identified two fisher populations for which we estimated effective population size (Ne) and genetic neighborhood size (NS). We calculated local genetic diversity measures [observed (Ho) and expected (He) heterozygosity, allelic richness (Ar), fixation index (FST), and number of migrants per generation (Nm)] and mapped continuous gradients of genetic diversity [Ar and inbreeding coefficient (FIS)] across the study area. We identified a fisher population in the West Cabinet Mountains [Ne of 26 (15.3–55.5), NS of 50–60] which is effectively isolated from the small population we detected in the Saint Joe/Coeur d'Alene Mountains [Ne of 6.5 (2.7–15), NS of 10–25]. We determined fisher have been effectively extirpated from the Selkirk and Purcell mountains and the lack of genetic connectivity between the two small remaining populations casts doubt on long term viability. Our study suggests northern Rockies fisher populations are vulnerable to landscape barriers and successful recovery will depend on future management and augmentation. We recommend these factors be considered when determining how, and if, species recovery should proceed. [ABSTRACT FROM AUTHOR]

Conservation efforts have preserved the southern white rhinoceros (SWR) in protected areas and have resulted in substantial overall growth in population size, but in small, fragmented populations in which inbreeding is an important risk. However, field observation of breeding often lacks sufficient accuracy to inform translocation strategies that are intended to increase genetic variation. The purpose of this study was to integrate microsatellite genotypes with an incomplete, field-observed pedigree to make inferences about mean kinship and basic demographic data that could be used to inform translocation programmes for SWR in a confined population in Botswana. Using this approach, we identified parents for 29 out of 45 offspring born in the reserve between 1993 and 2013 and detected eight non-breeding bulls with high mean kinship as candidates for translocation. The method also allowed inferences about demographic parameters that could influence the effectiveness of intervention strategies, such as age and timing of reproduction, and natal sex ratios. Importantly, the reproductive dominance of the bulls was not as skewed as expected after the original dominant bull was removed from the population, suggesting that closed populations can maintain multiple, simultaneously breeding males. The genetic data also confirmed that the accuracy of field-based parentage assignment was increased after implementation of an ear-notching programme. This study demonstrates the value of combining genetic information with ongoing surveillance to inform management of threatened populations, and of using mean kinship to inform metapopulation management by identifying candidates for translocation. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the genetic structure and diversity of populations of the yellow-bellied toad in Lower Saxony, Germany. These populations provide a good example of a fragmented distribution of amphibian pioneer species on the outer rim of their occurrence. In total, 150 individuals from 11 sites were genotyped using ten highly polymorphic microsatellites. The genetic diversity, as measured by allelic richness and heterozygosity, was lower than that of other European amphibian populations; the individuals could be assigned to five genetic clusters. The average genetic differentiation between populations was very high (mean FST = 0.27) and no migration was detected between the two major populations, which were about 50 km apart. Nonetheless, natural migration as well as translocations between some subpopulations could be detected. In one population, which was introduced in the 1970s, we were able to verify the potential source population of the introduced toads. The results are discussed in light of conservation management strategies applied to this highly endangered species. [ABSTRACT FROM AUTHOR]

Understanding patterns of speciation and subsequent gene flow can clarify the evolutionary origins and history of species endemic to a specific geographic region and reveal genetic patterns important for conservation and management of rare species. We chose Dicerandra from the North American Coastal Plain biodiversity hotspot as a model to explore these concepts because of its endemism and the threatened status of most of its species. Using microsatellite-based population-level analyses of 32 populations from four of the annual species (D. linearifolia var. linearifolia, D. linearifolia var. robustior, D. fumella, D. odoratissima, and D. radfordiana), we addressed questions of genetic diversity, population structure, and hybridization. Strong support was found for the species-level recognition of the recently described D. fumella from the Florida panhandle. Dicerandra linearifolia var. linearifolia showed some regional cohesion of populations, but there was no consistent geographic pattern to the clustering of populations. Dicerandra radfordiana showed consistent clustering with proximate populations of D. odoratissima. Given that D. radfordiana is found at the southeastern extreme of the range of D. odoratissima, these populations may represent the early stages of speciation by isolation. While there are morphological and bioclimatic niche distinctions between D. odoratissima and D. radfordiana, there is no molecular support for a distinct D. radfordiana. Overall, there is modest genetic diversity found at the population level for all Dicerandra annuals. Microsatellite data support previously proposed hypotheses of hybridization between D. linearifolia var. linearifolia and D. odoratissima, but do not support such hypotheses for D. fumella and D. linearifolia var. robustior. [ABSTRACT FROM AUTHOR]

Simple sequence repeat (SSR) markers are valuable for genetic and breeding applications, but SSR resources for the ornamental genus chrysanthemum (Chrysanthemum 3morifolium Ramat.) are still limited. Expressed sequence tags (ESTs) are sources of SSRs that represent an opportunity to develop SSRs to accelerate molecular breeding in chrysanthemum. In total, 4661 SSR loci were identified from 3823 SSR-containing unigenes in the chrysanthemum transcriptome with an average of one SSR per 6.98 kb. Of these SSR sequences, trinucleotide repeats (30.0%) predominated, followed by dinucleotide repeats (17.9%). In total, 1584 primer pairs were subsequently synthesized. By screening the parents and six individuals of the F1 progeny, 831 (52.5%) valid EST-SSR markerswere identified, of which 361 (43.4%) were polymorphic. The annotation of unigenes containing polymorphic SSRs indicated that 330 (93.5%) demonstrated significant homology to other plant protein sequences. Twenty-five polymorphic EST-SSR markers were further selected for transferability analysis and exhibited 93% amplification in six Ajania species and six other Chrysanthemum species. Based on genotyping of the 59 samples, neighbor-joining analysis revealed six phylogenetic groupings, which was confirmed by population structure analysis and principal component analysis (PCA). Phylogenetic relationships among the 59 samples revealed by SSRs were highly consistent with the traditional taxonomic classification of Chrysanthemum and Ajania. The polymorphism information content (PIC) values ranged from 0.29 to 0.86, with amean of 0.67, indicating high levels of informativeness. This research reveals the SSR distribution characteristics of chrysanthemum and provides a large number of new EST-SSR markers for further genetic diversity studies, genetic mapping, and molecular marker-assisted selection breeding for chrysanthemum. [ABSTRACT FROM AUTHOR]

Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of Ipomoea (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, and I. × leucantha) and understand the relationship among these species. Two satellite repeats (viz., Itf_1 and Itf_2) were identified from the diploid I. trifida genome sequence using RepeatExplorer on Galaxy. Together with the ribosomal DNA (rDNA), although without distinguishable chromosomes, a detailed karyotype was constructed for the six species. Our results showed a similar karyotype between I. tenuissima and I. × leucantha, indicating their close relationship. The signal distribution pattern of Itf_1, 45S rDNA combination, detected only in I. trifida, I. tabascana, and I. batatas, implied their close relationships. The chromosomes carrying 5S rDNA could be conserved among the six species as they always carried the Itf_2 signals, which generated a similar signal distribution pattern. The results enabled a detailed comparative cytogenetic analysis, providing valuable information to understand the relationship among these species and help assemble the genome sequence of the six species of Ipomoea. [ABSTRACT FROM AUTHOR]

Highlights • SSRs were used to identify fathers of tea individuals with valuable traits. • Paternity analyses showed that 8 individuals were derived from 'Ziyan' selfing. • The self-compatible 'Ziyan' is valuable for genetic studies and breeding in tea. Abstract Most tea plants (Camellia sinensis) are self-incompatible. Self-incompatibility is critical for preventing inbreeding depression and maintaining genetic diversity, but it can hinder breeding and genetic studies. Originally, the propose of this study was to identify fathers of 16 elite F 1 individuals derived from open-pollinated seeds of an anthocyanin-rich tea cultivar 'Ziyan'. In order to achieve this, 41 candidate parents and 16 F 1 individuals were genotyped with 15 polymorphic SSR markers. Using exclusion and likelihood methods, fathers of 12 individuals were identified at 95% level of confidence. Surprisingly, the results showed that eight individuals were from self-crossing of 'Ziyan'. Additional 36 SSR markers were used to further confirm selfing and the results were consistent, demonstrating that 'Ziyan' is self-compatible. As expected, the degrees of heterozygosity of the eight selfing individuals were significantly lower than 'Ziyan' and other tea accessions. This is the first report of a clonal cultivar of C. sinensis being self-compatible under open-pollination conditions and verified using DNA-based markers. Therefore, 'Ziyan' and its selfing offspring will be valuable materials for both genetic studies and breeding in C. sinensis. [ABSTRACT FROM AUTHOR]

Highlights • Simple protocol of Large-scale propagation of Prunus cerasifera was described. • Vigor vitroplants were produced, using Temporary Immersion Bioreactors. • The Temporary Immersion System improved the multiplication and rooting rates. • High percentage of genetic homogeneity of vitroplants was proved by ISSR analysis. Abstract An efficient protocol for the micropropagation of Prunus cerasifera using temporary immersion bioreactors was described. One-node cuttings excised from field-grown plants were successfully disinfected using 12% sodium hypochlorite for 10 min. Immersion duration, frequency and medium composition in Bioreactors type RITA® were evaluated. A high multiplication rate was obtained using RITA® bioreactors containing Murashige and Skoog's medium (MS) supplemented with 1 mg L−1 N6-benzyladenine (BAP) and 1 mg L−1 indole-3-butyric acid (IBA) with 20 min/12 h as immersion time. RITA®-derived shoots were found to be more vigorous than those regenerated using the standard procedure. Higher levels of photosynthetic pigments were observed in shoots cultured in bioreactors, during the proliferation and rooting stages, which proved a certain degree of photoautotrophy of RITA®-derived vitroplants. A high proportion of shoots was successfully rooted in an MS liquid medium supplemented with 1 g L−1 activated charcoal in RITA® bioreactors. During plant acclimatization, survival rates exceeding 80% were recorded. The genetic fidelity of micropropagated plants was investigated using inter simple sequence repeat (ISSR) markers. Results proved the generation of homogenous amplification profiles and thus supported the clonal fidelity of regenerated vitroplants. [ABSTRACT FROM AUTHOR]

The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously undescribed transposable element in Leishmania major (TATE element), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozoan genomes. [ABSTRACT FROM AUTHOR]

Sir4 is a core component of heterochromatin found in yeasts of the Saccharomycetaceae family, whose general hallmark is to harbor a three-loci mating-type system with two silent loci. However, a large part of the Sir4 amino acid sequences has remained unexplored, belonging to the dark proteome. Here, we analyzed the phylogenetic profile of yet undescribed foldable regions present in Sir4 as well as in Esc1, an Sir4-interacting perinuclear anchoring protein. Within Sir4, we identified a new conserved motif (TOC) adjacent to the N-terminal KU-binding motif. We also found that the Esc1-interacting region of Sir4 is a Dbf4-related H-BRCT domain, only present in species possessing the HO endonuclease and in Kluveryomyces lactis. In addition, we found new motifs within Esc1 including a motif (Esc1-F) that is unique to species where Sir4 possesses an H-BRCT domain. Mutagenesis of conserved amino acids of the Sir4 H-BRCT domain, known to play a critical role in the Dbf4 function, shows that the function of this domain is separable from the essential role of Sir4 in transcriptional silencing and the protection from HO-induced cutting in Saccharomyces cerevisiae. In the more distant methylotrophic clade of yeasts, which often harbor a two-loci mating-type system with one silent locus, we also found a yet undescribed H-BRCT domain in a distinct protein, the ISWI2 chromatin-remodeling factor subunit Itc1. This study provides new insights on yeast heterochromatin evolution and emphasizes the interest of using sensitive methods of sequence analysis for identifying hitherto ignored functional regions within the dark proteome. [ABSTRACT FROM AUTHOR]

A routine parentage test as part of a conservation program for Kiso horses identified a possible sex chromosome anomaly in a 7 months-old filly because of an aberrant result using LEX3, an X-linked marker. We then analyzed X-linked markers (LEX26, TKY38, and TKY270), Y-linked markers (Eca.YH12, Eca.YM2, Eca.YA16, and the sex-determining region Y gene), and an X/Y marker (Amelogenin gene). This analysis demonstrated that the filly had not inherited an X chromosome from her sire. A karyotyping analysis confirmed that the filly was 63, XO. As it was suspected that the horse would be sterile, we avoided using the horse as a broodmare; the information should also serve to prevent unnecessary conflict between owners transferring and receiving the horse. [ABSTRACT FROM AUTHOR]

Abstract The transduction of signal by the Notch receptors to the intracellular domain is highly regulated and relies on binding of the ligands to the Epidermal growth factor Like Repeats (ELRs) of receptor's extracellular domain. Both canonical and non-canonical ligands are known to interact with different ELRs and activate Notch receptors. The aim of this study was to investigate the interaction of a soluble non-canonical ligand, Y box-1 (Yb-1) with Notch3 receptor ELRs. Polyclonal antibodies were employed as novel tools to identify the binding site of this ligand. Using various ligand binding and signaling assays, soluble Yb-1 was found to interact specifically with the Notch3 receptor, but not with Notch1. The ELRs 17–24 of Notch3 were identified as the binding site for Yb-1. Further, Yb-1 and Notch3 ELRs 17–24 structures were modelled and the Yb-1-Notch3 interaction interface was predicted to be Notch3 ELRs 20–23. Binding of the Yb-1 with Notch3 ELRs different from those reported for canonical DSL ligands also transduced the signal to the intracellular domain through the negative regulatory region. In conclusion, study highlights the importance of molecular modifications in different Notch3 ELRs for the transduction of signal to the negative regulatory region. [ABSTRACT FROM AUTHOR]

Background: Repetitive DNA sequences (Repeats) are significant regions in the human genome that have a specific genomic distribution, structure, and several binding sites for genome architecture and function. In consequence, the possible configurations of Repeats in specific and dynamic regions like the gene promoters could define footprints for molecular mechanisms, pathways, and cell function beyond their density in the genome. Here we explored the distribution of Repeats in the upstream promoter region of the human coding genes with the aim to identify specific configurations, clusters and functional meaning of those elements. Our method includes structural descriptions, hierarchical clustering, pathway association, and functional enrichment analysis. Results: We report here several configurations of Repeats in the upstream promoter region (UPR), which define 2729 patterns for the 80% of the human coding genes. There are 47 types of Repeats in these configurations, where the most frequent were Alu, Low_complexity, MIR, Simple_repeat, LINE/L2, LINE/L1, hAT-Charlie, and ERV1. The distribution, length, and the high frequency of Repeats in the UPR defines several patterns and clusters, where the minimum frequency of configuration among Repeats was higher than 0.7. We found those clusters associated with cellular pathways and ontologies; thus, it was plausible to determine groups of Repeats to specific functional insights, for example, pathways for Genetic Information Processing or Metabolism shows particular groups of Repeats with specific configurations. Conclusion: Based on these findings, we propose that specific configurations of repetitive elements describe frequent patterns in the upstream promoter for sets of human coding genes, which those correlated to specific and essential cell pathways and functions. [ABSTRACT FROM AUTHOR]

Background: Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites. Results: The results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci. Conclusions: These observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS. [ABSTRACT FROM AUTHOR]

The wild tropical tasar silkworm, Antheraea mylitta polyphagous sericigenous lepidopteran insect, producing tasar silk of commercial importance is distributed in various parts of India as ecoraces, with variations in phenotypic traits like fecundity, voltinism, cocoon weight, silk ratio, etc. In spite of their superior quality silk, they encounter problems like their gradual decrease in number and identification. These populations are very difficult to separate based on morphological traits. The assessment of genetic structure of each population is considered as prerequisite for understanding and preserving natural biodiversity. Hence in the present investigation, genomic DNA of distinct populations of A. mylitta was extracted and screened for polymorphism by using EST-derived SSR markers. The DNA profiles based on these markers suggest that they could be effectively utilised for identifying the genetic variability among tasar ecoraces. The alignment of sequences obtained from genomic PCR products has identified potential EST-SSR marker to recognise single nucleotide polymorphism by comparing various tasar ecoraces [ABSTRACT FROM AUTHOR]

Background: Hereditary Non‐Polyposis Colorectal cancer is caused by Lynch Syndrome (LS; an autosomal dominant condition) or by Familial Colorectal Cancer Type‐X (FCCTX; a condition of high family risk that fulfills Amsterdam criteria). The lifetime risk of developing colorectal cancer (CRC) in FCCTX family members is high and CRC occurs later than in LS. Methods: To determine the impact of primary prevention colonoscopic screening in asymptomatic first‐degree relatives of incident CRC cases in 20 families with FCCTX, we compared cancer incidence and survival in 79 males and 83 females, assumed to be at 50% risk of inheriting a genetic CRC susceptibility factor, who entered screening to an unscreened control group from the families, matched for age at entry into screening and for sex. Results: In males, median age at entry into screening was 44.8 years, median follow‐up 12.4 years, 12% developed CRC, and 46% died after 30 years of follow‐up. Compared to the unscreened group, relative risk of CRC was 0.27 (95% confidence intervals (CI) 0.10–0.71). In screened females, comparable results were 44.5 years at entry, 11.2 years of follow‐up, 7.1% developed CRC, and 7.2% died after 30 years of follow‐up. The relative risk of CRC compared to the unscreened group was 0.19 (95% CI 0.07–0.48). Conclusion: Primary prevention screening colonoscopy in asymptomatic family members significantly decreased the risk of CRC in FCCTX. In male members of families with Familial Colorectal Type X who entered a screening colonoscopy program, the relative risk of colorectal cancer was 0.27 (95% CI 0.10–0.71) compared to unscreened male family members. In female members it was 0.19 (95% CI 0.07–0.48). [ABSTRACT FROM AUTHOR]

Background: Circulating cell-free fetal DNA (cffDNA) provides the opportunity for noninvasive prenatal diagnosis. Early knowledge of the fetal sex is essential in cases with a risk of a sex-linked genetic disease. A reliable and highly sensitive sex determination test is required for first trimester testing because of the low amounts of cffDNA. Methods: First trimester blood samples from 326 pregnant women were analyzed by real-time quantitative polymerase chain reaction (qPCR) for the presence of Y chromosome repetitive sequence (YRS). Blood samples were collected from gestational weeks 4-12. Fetal sex was predicted on the basis of results from the YRS assay of cffDNA extracted from maternal plasma. The predicted sex was compared with the phenotypic sex of the newborn baby (n = 294). Results: There was high concordance between the test results from the YRS assay and the actual sex at birth. There were no false-positive results, indicating agreement between male YRS results and male sex at birth. Two results were false negative (from gestational weeks 4 and 6) predicting female fetuses, when the actual sex at birth was male. Overall, the sensitivity of the YRS assay was 98.6% (95% CI, 95.1%-99.8%), specificity was 100% (95% CI, 97.5%-100%), and accuracy was 99.3% (95% CI, 97.5%-99.9%). From 7 weeks of gestation, sensitivity, specificity, and accuracy were 100%. Conclusions: This study shows that qPCR can be used to detect and quantify repetitive DNA sequences from 0.3 genome equivalents per milliliter of plasma. Prenatal sex determination by qPCR of YRS in cffDNA from maternal plasma was reliable and robust with cffDNA extracted from 1 mL of nonhemolyzed plasma, with a plasma equivalent per PCR of 167 μL. The YRS assay can be used for early noninvasive prenatal sex determination from a gestational age of 7 weeks. [ABSTRACT FROM AUTHOR]

Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome. [ABSTRACT FROM AUTHOR]

Msb069 primer pairs encompassed region is believed to be associated with a quantitative trait loci (QTL) of dorsal fin length in subgenus Poecilia. However, detailed investigation on Msb069 which originated from Xiphophorus on subgenus Poecilia remains unexplored. In this study, full sequence of Msb069 was characterized by sequencing bioinformatics analysis and gene expression. The sequence analysis of Msb069 primer pairs encompassed region on three species of Poecilia revealed higher number of microsatellite tandem repeats in Poecilia latipinna(ATG16) compared to P. sphenops(ATG13—14). There is no notable pattern of ATG tandem repeats discovered in the hybrids. The full sequence of Msb069 is 734 bp in length and showed a 233 bp conserved region between Xiphophorus and Poecilia. BLAST search performed on this sequence revealed no significant similarities. Nonquantitative RT-PCR exhibited the presence of Msb069 transcripts in three different tissues in subgenus Poecilia. Meanwhile, quantitative RT-PCR expression on two different tissues showed relatively higher expression of Msb069 transcript in P. latipinna dorsal fin tissues in both male and female fishes, suggesting a repressive function of this transcript with respect to dorsal fin length. However the exact gene expression event of Msb069 is still unknown and requires further investigation. [ABSTRACT FROM AUTHOR]

The cytoplasmic-genetic male sterility is the most widely used system for hybrid rice (Oryza sativa) seed production. It requires three lines: the two hybrid parents (A and R lines) and a third line (maintainer (B line)), which maintains the sterility of the female parent during seed increase. Studies were undertaken to identify maintainers and restorers for introduced cytoplasmic male sterile (CMS) lines using simple sequence repeat (SSR) markers and testcrosses. Molecular screening with SSR marker RM6100 grouped the assembled inbred lines into 30 potential restorers and 55 potential maintainers. One maintainer (WAS 127 -12-1-6-3-1) and 16 restorers were confirmed by testcrosses. WAS 127-12-1-2-3 had higher grain yield per plant in crosses with CMS1 (IR69625A) than the local checks (AgraRice and Jasmine 85) and could be used as a restorer to develop a locally adapted, high-yielding hybrid. Conversion of WAS 127 -12-1-6-3-1 into a local CMS line was stopped because of sterility instability in the BC1F1 generation. Continued testcrosses to the set of identified potential maintainers could help identify a stable one that can successfully be converted into a locally adapted CMS line. [ABSTRACT FROM AUTHOR]

A family of long intergenic noncoding RNA (lincRNA) genes, FAM230 is formed via gene sequence duplication, specifically in human chromosomal low copy repeats (LCR) or segmental duplications. This is the first group of lincRNA genes known to be formed by segmental duplications and is consistent with current views of evolution and the creation of new genes via DNA low copy repeats. It appears to be an efficient way to form multiple lincRNA genes. But as these genes are in a critical chromosomal region with respect to the incidence of abnormal translocations and resulting genetic abnormalities, the 22q11.2 region, and also carry a translocation breakpoint motif, several intriguing questions arise concerning the presence and function of the translocation breakpoint sequence in RNA genes situated in LCR22s. [ABSTRACT FROM AUTHOR]

Background: Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. Result: We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm the presence of two of these novel inversions. We show that there is a near linear relationship between the length of flanking IR and the minimum inversion size, without inverted repeats. Conclusion: The application of npInv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion. [ABSTRACT FROM AUTHOR]

LINE-1 (L1) is a non-long terminal repeat (LTR) retrotransposon inserted throughout the human genome. APOBEC3 (A3) proteins are part of a network of host intrinsic defenses capable of restricting retroviruses and the replication of L1 retroelements. These enzymes inactivate retroviruses primarily through deamination of single-stranded viral DNA. In contrast, only A3A deaminates L1 DNA, while the other six A3 proteins restrict L1 to varying degrees through yet poorly defined mechanisms. Here we provide further insight into the molecular attributes of L1 restriction by A3 proteins. We specifically investigated the roles of A3 protein oligomerization, interactions with RNA and their binding to the various L1 proteins. Our results show that compromising the ability of A3 proteins to oligomerize or interact with a nucleic acid substrate diminished L1 restriction to varying degrees. However the efficiency of their binding to L1 proteins did not predict restriction or the potency of the restriction. [ABSTRACT FROM AUTHOR]

Genetic variability can be generated through in vitro culture via somaclonal vari- ation. This tool can be potentially useful in a breeding program involving apomictic buffelgrass genotypes. The aim of this work was to evaluate inter simple sequence repeats (ISSR) as molecular markers to detect genetic variation in in vitro buffelgrass regenerated plants. Six plants regenerated from in vitro anther culture, via somatic embryogenesis were used, as well as the anther donor genotype (RN 51) as control. Of a total of 26 ISSR primers tested, 22 amplified, detecting 12% polymorphism with a divergence between 5 and 24% from RN 51. Amplification products were observed with the primers containing di-, tri- or tetra-nucleotide sequences, with or without additional nucleotides at the 3' end. The most informative primers were those containing the repetitive sequences GACAn, AGn or GAn. Moreover, the regenerants transplanted at field conditions differed in morphological characteristics among them and with respect to RN 51. This study confirms that ISSR are useful to identify genetic variability in in vitro regenerated buffelgrass plants. [ABSTRACT FROM AUTHOR]

Massive expansion of a DNA hexanucleotide sequence repeat (C2G4) within the human C9orf72 gene has been linked to a number of neurodegenerative diseases. In sodium or potassium salt solutions, single-stranded d(C2G4)n DNAs fold to form G-quadruplexes. We have found that in magnesium or lithium salt solutions, especially under slightly acidic conditions, d(C2G4)n oligonucleotides fold to form a distinctive higher order structure whose most striking feature is an “inverted” circular dichroism spectrum, which is distinguishable from the spectrum of the left handed DNA double-helix, Z-DNA. On the basis of CD spectroscopy, gel mobility as well as chemical protection analysis, we propose that this structure, which we call “iCD-DNA”, may be a left-handed Hoogsteen base-paired duplex, an unorthodox G-quadruplex/i-motif composite, or a non-canonical, “braided” DNA triplex. Given that iCD-DNA forms under slightly acidic solution conditions, we do not know at this point in time whether or not it forms within living cells. [ABSTRACT FROM AUTHOR]

Improvement of cotton fibre yield and quality is challenging due to the narrow genetic base of modern cotton cultivars, which emphasizes the great need to effectively explore the existing germplasm resources. With major objective to assess the genetic diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions (253 Chinese and 49 different exotic origins), were genotyped using 198 simple sequence repeats (SSRs) markers. Each of the 198 markers differed greatly in its ability to detect variations in the panel of cotton germplasm. The SSRs amplified 897 alleles, of which 77.7% were polymorphic. The number of alleles varied from 2 to 12 (mean 4.53). Gene diversity ranged from 0.020 to 0.492 with a mean of 0.279. The polymorphic information content (PIC) values ranged from 0.371 to 0.019 (mean 0.225). Genetic distances in the whole cotton germplasm ranged from 0.451 to 0.052 (mean 0.270), demonstrating relatively wider genetic diversity range. Chinese-origin cotton germplasm showed the highest level of SSR polymorphisms (gene diversity = 0.268, PIC = 0.218), whereas American-origin revealed the highest mean genetic distance (0.274). Model-based Bayesian analysis clustered the whole cotton germplasm into three subpopulations, and the highest molecular variation ws revealed between subpopulations (4%, P<0.001). The SSRs revealed moderate level of genetic diversity at DNA level, identified three structured subpopulations, suggesting a potential use of these markers for genomewide association mapping studies and for identifying and conserving useful alleles in upland cotton germplasm. [ABSTRACT FROM AUTHOR]

Habitat loss and fragmentation are threatening amphibians by increasing population isolation. However, artificial waterbodies created for livestock may contrast this phenomenon by providing surrogate habitats for amphibians. Here, we performed a genetic study on an amphibian species, Lissotriton vulgaris meridionalis, in a rural area in central Italy where natural wetlands are disappearing and drinking troughs for cattle watering are widespread. Specifically, we tested a panel of microsatellite markers to identify a suitable tool for addressing conservation genetic issues of this species that is undergoing severe local decline. Twelve of the 20 tested loci produced reliable amplifications and were polymorphic. Three distinct units with a low level of gene flow were distinguished and the population genetic structuring overlapped with geographic distribution. Such loci will be useful to assess the genetic diversity of the species across multiscale levels for its management and conservation. [ABSTRACT FROM AUTHOR]

Microsatellite loci were used for parentage identification of Odontobutis potamophila in five full-sib families. The combined exclusion probability of the first (E-1P) and the second parent (E-2P) revealed an obvious increase with the increase of number of microsatellite loci. The combined exclusion probability based on allele frequency suggested that at least eight microsatellite loci were needed for the identification of the 150 individuals from five families supported by the genetic distance analysis of individuals of these families. The double-blind test results indicated that the candidate individuals could find their correct parents through these loci thus eight microsatellite markers can be used for pedigree analysis of O. potamophlia in breeding industry as well as for future selection studies. [ABSTRACT FROM AUTHOR]

Background: Huntington’s disease (HD) is an autosomal-dominant neurodegenerative disorder with an average age at onset of 40 years. It is a polyglutamine (polyQ) disorder that is caused by an increase in the number of CAG repeats in the huntingtin (HTT) gene. Genetic tests that accurately determine the number of CAG repeats are performed for confirmation of diagnosis, predictive testing of persons at genetic risk for inheriting HD, and prenatal testing. The aim of our study was to evaluate efficacy of triplet-primed polymerase chain reaction (TP-PCR) for routine diagnosis of HD in suspected cases from India.Methods: We evaluated a combination of CAG flanking PCR and triplet-primed PCR for estimation of CAG repeats in 503 cases with clinical suspicion of HD.Results: There were 250 cases (49.7%) that showed the presence of expanded alleles, with 241 (47.9%) being fully penetrant alleles and nine (1.8%) in the reduced penetrance category. There were seven juvenile cases with an age of onset of < 20 years, with the longest allele comprising 106 CAG repeats found in an 8-year-old male patient. The results demonstrated an inverse (R = − 0.67) relationship between CAG length and age at clinical onset.Conclusion: Our study on pan-Indian cases is one of the largest studies reported so far in India and focuses on the most accurate and comprehensive molecular diagnostic evaluation of HD. [ABSTRACT FROM AUTHOR]

Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby ( cis ) or physically separated from ( trans ) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis - and trans -modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients. [ABSTRACT FROM AUTHOR]

Among the many candidate genes analyzed in eating disorder (ED) patients, those involved in dopaminergic functions may be of special relevance, as dopamine is known to play a significant role in feeding behavior, the distortion of body image, hyperactivity and reward and reinforcement processes. We aimed to determine the effect of functional polymorphisms and haplotypes in the Dopamine Receptor D4 ( DRD4 ) gene on general psychopathological symptoms in ED patients. Two-hundred-and-seventy-three ED patients [199 with Anorexia Nervosa (AN) and 74 with Bulimia Nervosa (BN)] completed the SCL-90R inventory and were genotyped for four functional, clinically relevant DRD4 polymorphisms: three variants in the promoter region [120-bp tandem repeat (TR, long vs. short allele), C-616G and C-521 T] and a variable number of tandem repeats (VNTR) in exon 3 (7R vs. non-7R allele). After correcting for multiple testing, none of the assayed polymorphisms were individually associated with SCL-90R results. Four DRD4 haplotypes ( *1–*4 ) were detected in the patients with a frequency > 0.1. In the BN group, haplotype *2 (non7R-TR long-C-C) was associated with higher scores in the three global SCL-90R indices (GSI, PSDI and PST) after Bonferroni correction ( p  ≤ 0.01 in all instances). Furthermore, carriers of this haplotype displayed higher scores (worst symptomatology) in Somatization , Obsessive-Compulsive , Anxiety , Phobic anxiety , Paranoid ideation and the test additional items ( p -values for the differences between carriers vs. non-carriers ranging from 0.0001 to 0.0110). Certain combinations of DRD4 variants may contribute to psychopathological features in BN patients. [ABSTRACT FROM AUTHOR]

Pathogenic Neisseria are responsible for significantly higher levels of morbidity and mortality than their commensal relatives despite having similar genetic contents. Neisseria possess a disparate arsenal of surface determinants that facilitate host colonisation and evasion of the immune response during persistent carriage. Adaptation to rapid changes in these hostile host environments is enabled by phase variation (PV) involving high frequency, stochastic switches in expression of surface determinants. In this study, we analysed 89 complete and 79 partial genomes, from the NCBI and Neisseria PubMLST databases, representative of multiple pathogenic and commensal species of Neisseria using PhasomeIt, a new program that identifies putatively phase-variable genes and homology groups by the presence of simple sequence repeats (SSR). We detected a repertoire of 884 putative PV loci with maxima of 54 and 47 per genome in gonococcal and meningococcal isolates, respectively. Most commensal species encoded a lower number of PV genes (between 5 and 30) except N. lactamica wherein the potential for PV (36–82 loci) was higher, implying that PV is an adaptive mechanism for persistence in this species. We also characterised the repeat types and numbers in both pathogenic and commensal species. Conservation of SSR-mediated PV was frequently observed in outer membrane proteins or modifiers of outer membrane determinants. Intermittent and weak selection for evolution of SSR-mediated PV was suggested by poor conservation of tracts with novel PV genes often occurring in only one isolate. Finally, we describe core phasomes—the conserved repertoires of phase-variable genes—for each species that identify overlapping but distinctive adaptive strategies for the pathogenic and commensal members of the Neisseria genus. [ABSTRACT FROM AUTHOR]

Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions. [ABSTRACT FROM AUTHOR]

Leucine-rich repeats and WD repeat domain-containing protein 1 (LRWD1) is implicated in the regulation of signal transduction, transcription, RNA processing and tumor development. However, LRWD1 transcriptional regulation is not fully understood. This study aimed to investigate the relationship between LRWD1 expression and reactive oxygen species (ROS) level in human embryonal carcinoma cell line, NT2/D1 cells, which will help in understanding the transcriptional regulatory role of ROS in cells. Results showed that the exposure of NT2/D1 cells to various concentrations of hydrogen peroxide (H 2 O 2 ) and the nitric oxide (NO) donor sodium nitroprusside (SNP) caused a significant increase in the mRNA and protein expression of LRWD1. In addition, LRWD1 promoter luciferase reporter assay, and Chromatin Immunoprecipitation assay (CHIP assay) showed that nuclear factor erythroid-2-related factor (Nrf2) was involved in the regulation of LRWD1 expression in response to oxidative stress. The involvement of Nrf2 was confirmed by shRNA-mediated knockdown of Nrf2 in NT2/D1 cells, which caused a significant decrease in LRWD1 expression in response to oxidative stress. Similarly, LRWD1 knockdown resulted in the accumulation of H 2 O 2 and superoxide anion radical (O2-). Blocking ROS production by N-acetyl cysteine (NAC) protected NT2/D1 shLRWD1cells from H 2 O 2 -induced cell death. Collectively, oxidative stress increased LRWD1 expression through a Nrf2-dependent mechanism, which plays an important role in cellular adaptation to oxidative stress. These results highlight an evidence, on the molecular level, about LRWD1 transcriptional regulation under oxidative stress. [ABSTRACT FROM AUTHOR]

Background: Prostate cancer is increasing among Iranian men and gene polymorphisms may play a role in the development of prostate cancer. Insulin-like growth factor 1 (IGF1) gene polymorphisms have been deeply explored in different malignancies. In this study, we aimed to explore the association of IGF1 CA repeat length polymorphism with the risk of prostate cancer development in Isfahan province of Iran. Method: The total blood of 100 prostate cancer patients and the equivalent matched control individuals were collected. DNA extraction was followed by IGF1 promoter polymorphism amplification. Genotyping was performed using polyacrylamide gel electrophoresis and sequencing was performed. Results: According to the results, IGF1 promoter polymorphic site showed six different alleles ranging from 17-22 CA repeats among our studied population. Comparing SL heterozygotes with both homozygotes, a significant increase in RR value (RR=4.5, p=0.031) was observed. Although age adjustment and family history did not elevate the RR value, but a significantly elevated risk of prostate cancer (RR= 3.143, p=0.002) was shown when we compared SS patients with LL ones according to their BPH history. Conclusion:In conclusion, carriers of (CA)17 allele could be at a higher risk of prostate cancer development and being SL heterozygotes could increase the risk of BPH development in our studied population. [ABSTRACT FROM AUTHOR]

Abstract: The utility of combining simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker genotyping was determined for genetically mapping a novel aphid (Aphis craccivora) resistance locus in cowpea breeding line SARC 1‐57‐2 and for introgressing the resistance into elite cultivars by marker‐assisted backcrossing (MABC). The locus was tagged with codominant SSR marker CP 171F/172R with a recombination fraction of 5.91% in an F2 population from ‘Apagbaala’ x SARC 1‐57‐2. A SNP‐genotyped biparental recombinant inbred line population was genotyped for CP 171F/172R, which was mapped to position 11.5 cM on linkage group (LG) 10 (physical position 30.514 Mb on chromosome Vu10). Using CP 171F/172R for foreground selection and a KASP‐SNP‐based marker panel for background selection in MABC, the resistance from SARC 1‐57‐2 was introduced into elite susceptible cultivar ‘Zaayura’. Five BC4F3 lines of improved ‘Zaayura’ that were isogenic except for the resistance locus region had phenotypes similar to SARC 1‐57‐2. This study identified a novel aphid resistance locus and demonstrated the effectiveness of integrating SSR and SNP markers for trait mapping and marker‐assisted breeding. [ABSTRACT FROM AUTHOR]

Premise of the Study: To enhance the understanding of the recent invasion process of the clonal waterweed Elodea nuttallii (Hydrocharitaceae), analyses of population structure and genotypic diversity need to be undertaken, for which genetic markers are needed. Methods and Results: High‐throughput sequencing of DNA enriched for microsatellites was used to develop 24 loci that were characterized in E. nuttallii, 21 of which were polymorphic, with the number of alleles ranging from two to 10. In two populations, expected heterozygosity ranged among loci between zero and 0.796. In the congener E. canadensis, all markers yielded PCR products, 19 of which were polymorphic, with two to nine alleles and expected heterozygosity ranging from zero to 0.690 in two populations. Conclusions: The markers described should be useful for future studies of population structure and clonal diversity of E. nuttallii as well as E. canadensis in their native and invasive range. [ABSTRACT FROM AUTHOR]

Plague, caused by Yersinia pestis, was classified as a reemerging infectious disease by the World Health Organization. The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province, China. Thereafter, continuous wild rodent plague (sylvatic plague) was identified as the main plague reservoir of this focus. In this study, the epizootics in Yulong focus were described, and three molecular typing methods, including the different region (DFR) analysis, clustered regularly interspaced short palindromic repeats (CRISPRs), and the multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) (14+12), were used for the molecular typing and source tracing of Y. pestis isolates in the Yulong plague focus. Simultaneously, several isolates from the vicinity of Yunnan were used as controls. The results showed that during the 10-year period from 2006 to 2016, an animal plague epidemic occurred in 6 of those years, and 5 villages underwent an animal plague epidemic within a 30-km2 area of the Yulong plague focus. Searching for dead mice was the most effective monitoring method in this plague focus. No positive sample has been found in 6937 captured live rodents thus far, suggesting that the virulence of strains in the Yulong plague focus is stronger and the survival time of mice is shorter after infection. Strains from Lijiang, Sichuan and Tibet were of the same complex based on a typing analysis of DFR and CRISPR. The genetic relationship of Y. pestis illustrated by MLVA “14+12” demonstrates that Tibet and Sichuan strains evolved from the strains 1.IN2 (Qinghai, 1970 and Tibet, 1976), and Lijiang strains are closer to Batang strains (Batang County in Sichuan province, 2011, Himalaya marmot plague foci) in terms of genetic or phylogenic relationships. In conclusion, we have a deeper understanding of this new plague focus throughout this study, which provides a basis for effective prevention and control. [ABSTRACT FROM AUTHOR]

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. [ABSTRACT FROM AUTHOR]

Deschampsia antactica E. Desv. is one of the only two native vascular plants of Antarctica, having a disjunct distribution with South America. Its presence in different environmental conditions turns it into an interesting evolution model, particularly for genomic evolutionary studies. The repetitive DNA is a genome component that cause important changes in genome size and chromosome organization, and therefore, its variation is very important in group’s delimitation. Some tandem repetitive DNA sequences, known as satellite DNA (satDNAs) are shared between many groups of Poaceae (e.g., of these are the CON1, CON2, COM1, and COM2 sequences) highlighting its evolutionary component. This study aims to identify, classify, and characterize repetitive elements in the D. antarctica genome by clustering analysis of genome sequences, focusing on the CON1, CON2, COM1, and COM2. Repetitive DNA represented about 73.3% of the D. antarctica genome. All studied populations presented loci for the studied satDNAs but the distribution pattern showed differences that seem to be related to the geographic distribution. The analysis of CON/COM sequences in D. antarctica contributes to the understanding of these elements in Poaceae genomes and highlights the importance of changes in chromosome organization of repetitive DNA in populations with fragmented geographical distribution. The distribution of such chromosome changes may both reflect the process of colonization of D. antarctica in Antarctica and explain some evolutionary processes of differentiation in Deschampsia species complex in the Patagonia, which is still unresolved with other DNA sequences. [ABSTRACT FROM AUTHOR]

Single-nucleotide polymorphisms (SNPs), microsatellites and copy number variation (CNV) were studied on the Y chromosome to understand the paternal origin and phylogenetic relationships for resource protection, rational development and utilization of the domestic Bactrian camel in China. Our sample set consisted of 94 Chinese domestic Bactrian camels from four regions (Inner Mongolia, Gansu, Qinghai and Xinjiang), we screened 29 Y-chromosome-specific loci for SNPs, analysed 40 bovine-derived microsatellite loci and measured CNVs of HSFY and SRY through Sanger sequencing, automated fluorescence-based microsatellite analysis and quantitative real-time PCR, respectively. A multicopy gene, SRY, was first found, and sequence variation was only detected in SRY in a screen of 29 loci in 13 DNA pools of individual camels. In addition, a TG repeat in the USP9Y gene was identified as the first polymorphic microsatellite in the camel Y chromosome, whereas microsatellite based on bovine sequences were not detected. The frequency of each allele varied among different populations. For the Nanjiang, Hexi and Alashan populations, a 243-bp allele was found. For the Sunite population, 241-bp, 243-bp and 247-bp alleles were detected, and the frequencies of these alleles were 22.2%, 44.5% and 33.3%, respectively; 241-bp and 243-bp alleles were found in other populations. Finally, CNVs in two Y-chromosomal genes were detected; CNV for HSFY and SRY ranged from 1 to 3 and from 1 to 9, respectively. [ABSTRACT FROM AUTHOR]

The Neotropical fish, Hoplias malabaricus, is one of the most cytogenetically studied fish taxon with seven distinct karyomorphs (A–G) comprising varying degrees of sex chromosome differentiation, ranging from homomorphic to highly differentiated simple and multiple sex chromosomes. Therefore, this fish offers a unique opportunity to track evolutionary mechanisms standing behind the sex chromosome evolution and differentiation. Here, we focused on a high-resolution cytogenetic characterization of the unique XX/XY1Y2 multiple sex chromosome system found in one of its karyomorphs (G). For this, we applied a suite of conventional (Giemsa-staining, C-banding) and molecular cytogenetic approaches, including fluorescence in situ hybridization FISH (with 5S and 18S rDNAs, 10 microsatellite motifs and telomeric (TTAGGG)n sequences as probes), comparative genomic hybridization (CGH), and whole chromosome painting (WCP). In addition, we performed comparative analyses with other Erythrinidae species to discover the evolutionary origin of this unique karyomorph G-specific XY1Y2 multiple sex chromosome system. WCP experiments confirmed the homology between these multiple sex chromosomes and the nascent XX/XY sex system found in the karyomorph F, but disproved a homology with those of karyomorphs A–D and other closely related species. Besides, the putative origin of such XY1Y2 system by rearrangements of several chromosome pairs from an ancestral karyotype was also highlighted. In addition, clear identification of a male-specific region on the Y1 chromosome suggested a differential pattern of repetitive sequences accumulation. The present data suggested the origin of this unique XY1Y2 sex system, revealing evidences for the high level of plasticity of sex chromosome differentiation within the Erythrinidae. [ABSTRACT FROM AUTHOR]

Abstract: Recent developments in, and widespread availability of, platforms, technologies, and computer software and hardware have enhanced the use of genetic markers to address major scientific questions in non‐model organisms, even by researchers with limited expertise in genomics. However, there are few studies investigating the genomes of non‐model insects using these approaches. This review discusses the application of next‐generation sequencing (NGS) technologies to the study of genomes of wild organisms. We first introduce currently available NGS‐based methods—including restriction site‐associated DNA sequencing; multiplexed inter‐simple sequence repeat genotyping by sequencing; target capture; and amplicon, transcriptome, and whole genome sequencing—as useful tools for studies of non‐model insects. We also provide guidelines for first‐time users of NGS systems. In addition to the massive amount of information that it provides, a major advantage of NGS data is the scalability to future research projects. Studies using NGS technology can answer questions related to basic entomology by focusing on the unique nature of non‐model insects in wild environments in a way that is not possible for model organisms. [ABSTRACT FROM AUTHOR]

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE=0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10-3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region. [ABSTRACT FROM AUTHOR]

Scab caused by the fungus Venturia inaequalis (Cook) G. Winter is the most devastating disease of the apple worldwide. To control the disease most efforts have been directed toward the breeding programmes by introgression of scab resistance genes from wild apples into commercial cultivars. Although, various apple genotypes exist in Iran, no comprehensive data regarding the possible presence of scab resistance genes is available. In this research the presence of five R genes ( Rvi2 , Rvi4 , Rvi6 , Rvi8 and Rvi11 ) was assessed in 28 wild and domestic apple genotypes using 13 SCAR and SSR markers. Sequencing and blastN results confirmed the identify of Rvi2 , Rvi6 , Rvi8 and Rvi11 genes. Based on the results, wild apples had more resistance genes and among foreign and autochthonous apples, ‘Golden Delicious’, ‘Malayer-1’ and ‘Shahroud-6’ carrying at least three R genes categorized as almost tolerant cultivars. However, ‘Gala’, ‘Boshghabi-e Damavand’, ‘Manouchehri’ and ‘Golab’ had just one R gene and classified as susceptible cultivars. The most frequent scab resistance breeding programmes rely on Rvi6 gene ( HcrVf2 gene), which was also detected in this study in crabapple Malus floribunda providing a rich resource for developing resistant apple cultivars in Iran. [ABSTRACT FROM AUTHOR]