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Songbirds have an unusual genomic element which is only found in their germline cells, known as the germline-restricted chromosome (GRC). Because germ cells contain both GRC and non-GRC (or A-chromosome) sequences, confidently identifying the GRC-derived elements from genome assemblies has proven difficult. Here, we introduce a new application of a transcriptomic method for GRC sequence identification. By adapting the Stringtie/Ballgown pipeline to use somatic and germline DNA reads, we find that the ratio of fragments per kilobase per million mapped reads can be used to confidently assign contigs to the GRC. Using this comparative coverage analysis, we successfully identify 733 contigs as high confidence GRC sequences (720 newly identified in this study) and 51 contigs which were validated using quantitative polymerase chain reaction. We also identified two new GRC genes, one hypothetical protein and one gene encoding an RNase H-like domain, and placed 16 previously identified but unplaced genes onto their host contigs. With the current focus on sequencing GRCs from different songbirds, our work adds to the genomic toolkit to identify GRC elements, and we provide a detailed protocol and GitHub repository at https://github.com/brachtlab/Comparative%5fCoverage%5fAnalysis (last accessed May 12, 2021). [ABSTRACT FROM AUTHOR]

High levels of heterozygosity present a unique genome assembly challenge and can adversely impact downstream analyses, yet is common in sequencing datasets obtained from non-model organisms. Here we show that by re-assembling a heterozygous dataset with variant parameters and different assembly algorithms, we are able to generate assemblies whose protein annotations are statistically enriched for specific gene ontology categories. While total assembly length was not significantly affected by assembly methodologies tested, the assemblies generated varied widely in fragmentation level and we show local assembly collapse or expansion underlying the enrichment or depletion of specific protein functional groups. We show that these statistically significant deviations in gene ontology groups can occur in seemingly high-quality assemblies, and result from difficult-to-detect local sequence expansion or contractions. Given the unpredictable interplay between assembly algorithm, parameter, and biological sequence data heterozygosity, we highlight the need for better measures of assembly quality than N50 value, including methods for assessing local expansion and collapse. Author summary: In the genomic era, genomes must be reconstructed from fragments using computational methods, or assemblers. How do we know that a new genome assembly is correct? This is important because errors in assembly can lead to downstream problems in gene predictions and these inaccurate results can contaminate databases, affecting later comparative studies. A particular challenge occurs when a diploid organism inherits two highly divergent genome copies from its parents. While it is widely appreciated that this type of data is difficult for assemblers to handle properly, here we show that the process is prone to more errors than previously appreciated. Specifically, we document examples of regional expansion and collapse, affecting downstream gene prediction accuracy, but without changing the overall genome assembly size or other metrics of accuracy. Our results suggest that assembly evaluation methods should be altered to identify whether regional expansions and collapses are present in the genome assembly. [ABSTRACT FROM AUTHOR]

One of the leading causes for the development of adverse metabolic effects, including type 2 diabetes, dyslipidemia, and cardiovascular diseases, is the accumulation of excess body weight, often measured by body mass index (BMI). Although BMI, calculated using weight and height, is the standard measure used to determine body adiposity in clinical and public health guidelines, an inherent limitation is that BMI does not distinguish where in the body adiposity is deposited. Central obesity, characterized by greater accumulation of adiposity in the abdominal region, has been associated with a higher risk of mortality, independent of BMI. Importantly, one of the determinants of body fat distribution is sex hormones. Both estrogens and androgens appear to directly and indirectly influence body fat distribution. Our review will focus specifically on the role of estrogens and their influence in determining body fat distribution and overall health of adipose tissues, and the role of epigenetic mechanisms in regulating the production and function of estrogens. [ABSTRACT FROM AUTHOR]

We recently sequenced the genome of the first subterrestrial metazoan, the nematode Halicephalobus mephisto. A central finding was a dramatic expansion of genes encoding avrRpt2 induced gene (AIG1), and 70 kDa heat shock (Hsp70) domains. While the role of Hsp70 in thermotolerance is well established, the contribution of AIG1 is much more poorly characterized, though in plants some members of this family are heat-induced. Hypothesizing that this dual domain expansion may constitute a general biosignature of thermal stress adaptation, here we examine a number of genomes, finding that expansion of both AIG1 and Hsp70 is common in bivalves. Phylogenetic analysis reveals that the bivalve-specific Hsp70 protein expansion groups with H. mephisto sequences. Our identification of the same gene expansions in bivalves and a nematode implies that this biosignature may be a general stress adaptation strategy for protostomes, particularly those organisms that cannot escape their stressful environments. We hypothesize that the two families play largely complementary mechanistic roles, with Hsp70 directly refolding heat-denatured proteins while AIG1 promotes cellular and organismal survival by inhibiting apoptosis. [ABSTRACT FROM AUTHOR]

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor ''silent'' germline micronuclear genome by a process of ''unscrambling'' and fragmentation. The tiny macronuclear ''nanochromosomes'' typically encode single, proteincoding genes (a small portion, 10%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. [ABSTRACT FROM AUTHOR]

A conference paper about de novo cytosine methylation and hydroxymethylation in the Oxytricha trifallax is presented. It mentions that DNA methyltransferase inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence, which elevates the level of germline limited repetitive elements in cells. It found a link between cytosine DNA methylation and genome stability which shows the ability of the cells to methylate aberrant chromosomes.

Diversity within science, technology, engineering, and mathematics (STEM) remains disturbingly low. Relative to larger, highly funded universities, smaller schools harbor more diverse student demographics and more limited resources. Here, we propose four strategies leveraging the unique advantages of smaller institutions to advance underrepresented scholars along STEM pathways. [ABSTRACT FROM AUTHOR]

Summary Developmentally programmed genome rearrangements are rare in vertebrates, but have been reported in scattered lineages including the bandicoot, hagfish, lamprey, and zebra finch ( Taeniopygia guttata ) [ 1 ]. In the finch, a well-studied animal model for neuroendocrinology and vocal learning [ 2 ], one such programmed genome rearrangement involves a germline-restricted chromosome, or GRC, which is found in germlines of both sexes but eliminated from mature sperm [ 3, 4 ]. Transmitted only through the oocyte, it displays uniparental female-driven inheritance, and early in embryonic development is apparently eliminated from all somatic tissue in both sexes [ 3, 4 ]. The GRC comprises the longest finch chromosome at over 120 million base pairs [ 3 ], and previously the only known GRC-derived sequence was repetitive and non-coding [ 5 ]. Because the zebra finch genome project was sourced from male muscle (somatic) tissue [ 6 ], the remaining genomic sequence and protein-coding content of the GRC remain unknown. Here we report the first protein-coding gene from the GRC: a member of the α-soluble N- ethylmaleimide sensitive fusion protein (NSF) attachment protein (α-SNAP) family hitherto missing from zebra finch gene annotations. In addition to the GRC-encoded α-SNAP, we find an additional paralogous α-SNAP residing in the somatic genome (a somatolog)—making the zebra finch the first example in which α-SNAP is not a single-copy gene. We show divergent, sex-biased expression for the paralogs and also that positive selection is detectable across the bird α-SNAP lineage, including the GRC-encoded α-SNAP. This study presents the identification and evolutionary characterization of the first protein-coding GRC gene in any organism. [ABSTRACT FROM AUTHOR]