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1. The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo

   https://doi.org/10.1093/molbev/msx057  

   Gubala, Anna M. ; Schmitz, Jonathan F. ; Kearns, Michael J. ; Vinh, Tery T. ; Bornberg-Bauer, Erich ; Wolfner, Mariana F. ; Findlay, Geoffrey D. ( May 2017 , Molecular biology and evolution)

   New genes arise through a variety of mechanisms, including the duplication of existing genes and the de novo birth of genes from noncoding DNA sequences. While there are numerous examples of duplicated genes with important func- tional roles, the functions of de novo genes remain largely unexplored. Many newly evolved genes are expressed in the male reproductive tract, suggesting that these evolutionary innovations may provide advantages to males experiencing sexual selection. Using testis-specific RNA interference, we screened 11 putative de novo genes in Drosophila mela- nogaster for effects on male fertility and identified two, goddard and saturn, that are essential for spermatogenesis and sperm function. Goddard knockdown (KD) males fail to produce mature sperm, while saturn KD males produce few sperm, and these function inefficiently once transferred to females. Consistent with a de novo origin, both genes are identifiable only in Drosophila and are predicted to encode proteins with no sequence similarity to any annotated protein. However, since high levels of divergence prevented the unambiguous identification of the noncoding sequences from which each gene arose, we consider goddard and saturn to be putative de novo genes. Within Drosophila, both genes have been lost in certain lineages, but show conserved, male-specific patterns of expression in the species in which they are found. Goddard is consistently found in single-copy and evolves under purifying selection. In contrast, saturn has diversified through gene duplication and positive selection. These data suggest that de novo genes can acquire essential roles in male reproduction. 

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2. Structural and functional characterization of a putative de novo gene in Drosophila

   https://doi.org/10.1038/s41467-021-21667-6  

   Lange, Andreas ; Patel, Prajal H. ; Heames, Brennen ; Damry, Adam M. ; Saenger, Thorsten ; Jackson, Colin J. ; Findlay, Geoffrey D. ; Bornberg-Bauer, Erich ( December 2021 , Nature Communications)

   null (Ed.)

   Abstract Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard , a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α -helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years. 

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3. A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

   https://doi.org/10.1371/journal.pgen.1009787  

   Rivard, Emily L. ; Ludwig, Andrew G. ; Patel, Prajal H. ; Grandchamp, Anna ; Arnold, Sarah E. ; Berger, Alina ; Scott, Emilie M. ; Kelly, Brendan J. ; Mascha, Grace C. ; Bornberg-Bauer, Erich ; et al ( September 2021 , PLOS Genetics)

   Malik, Harmit S. (Ed.)

   Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas , required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas . The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis. 

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4. Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions

   https://doi.org/10.1093/genetics/iyad010  

   Hoerr, Remington E. ; Eng, Alex ; Payen, Celia ; Di Rienzi, Sara C. ; Raghuraman, M. K. ; Dunham, Maitreya J. ; Brewer, Bonita J. ; Friedman, Katherine L. ; Rusche, ed., L. ( January 2023 , GENETICS)

   Evolution is driven by the accumulation of competing mutations that influence survival. A broad form of genetic variation is the amplification or deletion of DNA (≥50 bp) referred to as copy number variation (CNV). In humans, CNV may be inconsequential, contribute to minor phenotypic differences, or cause conditions such as birth defects, neurodevelopmental disorders, and cancers. To identify mechanisms that drive CNV, we monitored the experimental evolution of Saccharomyces cerevisiae populations grown under sulfate-limiting conditions. Cells with increased copy number of the gene SUL1, which encodes a primary sulfate transporter, exhibit a fitness advantage. Previously, we reported interstitial inverted triplications of SUL1 as the dominant rearrangement in a haploid population. Here, in a diploid population, we find instead that small linear fragments containing SUL1 form and are sustained over several generations. Many of the linear fragments are stabilized by de novo telomere addition within a telomere-like sequence near SUL1 (within the SNF5 gene). Using an assay that monitors telomerase action following an induced chromosome break, we show that this region acts as a hotspot of de novo telomere addition and that required sequences map to a region of <250 base pairs. Consistent with previous work showing that association of the telomere-binding protein Cdc13 with internal sequences stimulates telomerase recruitment, mutation of a four-nucleotide motif predicted to associate with Cdc13 abolishes de novo telomere addition. Our study suggests that internal telomere-like sequences that stimulate de novo telomere addition can contribute to adaptation by promoting genomic plasticity.

    

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5. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect

   https://doi.org/10.1111/mec.13578  

   Standage, Daniel S. ; Berens, Ali J. ; Glastad, Karl M. ; Severin, Andrew J. ; Brendel, Volker P. ; Toth, Amy L. ( March 2016 , Molecular Ecology)

   Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insectPolistes dominula, accompanied by analysis of caste‐related transcriptome and methylome sequence data for adult queens and workers.Polistes dominulapossesses a fairly typical hymenopteran genome, but shows very low genomewideGCcontent and some evidence of reduced genome size. We found numerous caste‐related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these –omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects:DNAmethylation. Along with a conspicuous loss of a key gene associated with environmentally responsiveDNAmethylation (the de novoDNAmethyltransferaseDnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative –omics data for this important behavioural and evolutionary model system call into question the general importance ofDNAmethylation in caste differences and evolution in social insects.

    

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