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

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

10.1101/2021.06.10.447990 ◽

2021 ◽

Author(s):

Emily L. Rivard ◽

Andrew G. Ludwig ◽

Prajal H. Patel ◽

Anna Grandchamp ◽

Sarah E. Arnold ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Male Fertility ◽

De Novo ◽

Developmental Process ◽

Chromatin Condensation ◽

Protein Coding ◽

Non Coding Rna ◽

De Novo Genes ◽

History Of ◽

Redundant Role

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 show 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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Comparison among the first representative chloroplast genomes of Orontium, Lasia, Zamioculcas, and Stylochaeton of the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

10.1101/2020.04.07.029389 ◽

2020 ◽

Author(s):

Abdullah ◽

Claudia L. Henriquez ◽

Furrukh Mehmood ◽

Iram Shahzadi ◽

Zain Ali ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

History Of ◽

Contraction And Expansion ◽

Insight Into

AbstractThe chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of the first representatives of four genera representing three subfamilies: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using the plastomes. The size of the chloroplast genomes ranged from 163,770–169,982 bp. These genomes comprise 114 unique genes, including 80 protein-coding, 4 rRNA, and 30 tRNA genes. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The junctions JSB (IRb/SSC) and JSA (SSC/IRa) are highly variable, as is oligonucleotide repeats content among the genomes. The patterns of inverted repeats contraction and expansion were shown to be homoplasious and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were shown for several genes in S. bogneri. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

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NOVEL INTRONIC NON-CODING RNAS CONTRIBUTE TO MAINTENANCE OF PHENOTYPE IN SACCHAROMYCES CEREVISIAE

10.1101/033076 ◽

2015 ◽

Author(s):

Katarzyna B Hooks ◽

Samina Naseeb ◽

Sam Griffiths-Jones ◽

Daniela Delneri

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Structure ◽

Structure Prediction ◽

De Novo ◽

Intron Retention ◽

Intron Loss ◽

Common Belief ◽

Rna Structures ◽

Protein Coding ◽

Non Coding Rna

The Saccharomyces cerevisiae genome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel non-coding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employed de novo RNA structure prediction tools to screen intronic sequences in S. cerevisiae and 36 other fungi. We identified and validated 19 new intronic RNAs via RNAseq and RT-PCR. Contrary to common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In other two cases we showed that the ncRNAs were further processed from their introns. RNAseq analysis confirmed higher expression of introns in the ribosomial protein genes containing predicted RNA structures. We deleted the novel intronic RNA structure within the GLC7 intron and showed that this predicted ncRNA, rather than the intron itself, is responsible for the cell???s ability to respond to salt stress. We also showed a direct association between the presence of the intronic ncRNA and GLC7 expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbour functional ncRNAs.

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De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

10.1101/461483 ◽

2018 ◽

Cited By ~ 1

Author(s):

Federico Vita ◽

Amedeo Alpi ◽

Edoardo Bertolini

Keyword(s):

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Rna Seq ◽

Genetic Studies ◽

Protein Coding ◽

Important Species ◽

White Truffle ◽

Tuber Magnatum ◽

Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

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Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

Nucleic Acids Research ◽

10.1093/nar/gkz1080 ◽

2019 ◽

Vol 48 (1) ◽

pp. 290-303 ◽

Cited By ~ 7

Author(s):

Christopher E Ellison ◽

Weihuan Cao

Keyword(s):

Drosophila Melanogaster ◽

Evolutionary Dynamics ◽

De Novo ◽

Population Level ◽

Chromosome Length ◽

Nanopore Sequencing ◽

Long Reads ◽

Wild Strains ◽

Genome Assemblies ◽

Insight Into

Abstract Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.

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Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

Plants ◽

10.3390/plants9060737 ◽

2020 ◽

Vol 9 (6) ◽

pp. 737 ◽

Cited By ~ 2

Author(s):

Abdullah ◽

Claudia L. Henriquez ◽

Furrukh Mehmood ◽

Iram Shahzadi ◽

Zain Ali ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

History Of ◽

And Bisexual ◽

Contraction And Expansion

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

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Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation

Scientific Reports ◽

10.1038/s41598-021-81784-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mingzheng Duan ◽

Haiying Bao ◽

Tolgor Bau

Keyword(s):

Life History ◽

De Novo ◽

Phylogenetic Analyses ◽

Gene Families ◽

Single Copy ◽

Mushroom Species ◽

Protein Coding ◽

Homologous Genes ◽

Metabolic Genes ◽

History Of

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.

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Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster

BMC Microbiology ◽

10.1186/s12866-021-02168-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lucas P. Henry ◽

Julien F. Ayroles

Keyword(s):

Drosophila Melanogaster ◽

Bacterial Diversity ◽

Experimental Evolution ◽

Host Selection ◽

Meta Analysis ◽

History Of ◽

Fundamental Insight ◽

Host Evolution ◽

Genomic Basis ◽

Insight Into

Abstract Background Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection. Results Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. Conclusions Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.

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Comparative Chloroplast Genomics in Phyllanthaceae Species

Diversity ◽

10.3390/d13090403 ◽

2021 ◽

Vol 13 (9) ◽

pp. 403

Author(s):

Umar Rehman ◽

Nighat Sultana ◽

Abdullah ◽

Abbas Jamal ◽

Maryam Muzaffar ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Single Copy ◽

Protein Coding ◽

Coding Sequences ◽

Tropical Regions ◽

Chloroplast Genomes ◽

The Family ◽

Insight Into ◽

Small Single Copy

Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, and trees that are mostly distributed in tropical regions. Here, we elucidate the molecular evolution of the chloroplast genome in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference. We de novo assembled the chloroplast genomes of three Phyllanthaceae species, i.e., Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius, and compared them with six other previously reported genomes. All species comprised two inverted repeat regions (size range 23,921–27,128 bp) that separated large single-copy (83,627–89,932 bp) and small single-copy (17,424–19,441 bp) regions. Chloroplast genomes contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, and 4 rRNAs. The deletion/pseudogenization of rps16 genes was found in only two species. High variability was seen in the number of oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions were similar. The transition substitutions were higher in coding sequences than in non-coding sequences. Phylogenetic analysis revealed the polyphyletic nature of the genus Phyllanthus. The polymorphic protein-coding genes, including rpl22, ycf1, matK, ndhF, and rps15, were also determined, which may be helpful for reconstructing the high-resolution phylogenetic tree of the family Phyllanthaceae. Overall, the study provides insight into the chloroplast genome evolution in Phyllanthaceae.

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Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence

Genome Biology and Evolution ◽

10.1093/gbe/evaa127 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1355-1366

Author(s):

Karina Zile ◽

Christophe Dessimoz ◽

Yannick Wurm ◽

Joanna Masel

Keyword(s):

Drosophila Melanogaster ◽

De Novo ◽

Experimental Studies ◽

High Confidence ◽

Protein Coding ◽

Noncoding Sequences ◽

De Novo Genes ◽

Intergenic Sequences ◽

Drosophila Melanogaster Subgroup ◽

Reading Frames

Abstract Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.

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