Protein evidence of unannotated ORFs in Drosophila reveals unappreciated diversity in the evolution of young proteins DOI Creative Commons
Eric B Zheng, Li Zhao

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: April 5, 2022

Abstract De novo gene origination, where a previously non-genic genomic sequence becomes genic through evolution, has been increasingly recognized as an important source of evolutionary novelty across diverse taxa. Many de genes have proposed to be protein-coding, and in several cases experimentally shown yield protein products. However, the systematic study proteins hampered by doubts regarding translation their transcripts without experimental observation Using systematic, ORF-focused mass-spectrometry-first computational approach, we identify almost 1000 unannotated open reading frames with evidence (utORFs) model organism Drosophila melanogaster , 371 which canonical start codons. To quantify comparative similarity these utORFs infer phylostratigraphic age, further develop synteny-based approach. Combining results reference datasets on tissue- life-stage-specific transcription conservation, different properties amongst utORFs. Contrary expectations, fastest-evolving are not youngest evolutionarily. We observed more brain than testis. Most identified may origin, even accounting for possibility false-negative detection. Finally, divergence after inferred origin event remains substantial, raising that turn over frequently. Our suggest there is substantial unappreciated diversity evolution: many exist appreciated; divergent trajectories; gained lost All all, single characteristic but rather complex origins trajectories proteins. Impact statement The analysis mass-spectrometry data all possible reveals evolutionarily young, distinct characters.

Language: Английский

De novo gene integration into regulation networks via interaction with conserved genes in peach DOI Creative Commons
Yunpeng Cao,

Jiayi Hong,

Yun Zhao

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(12)

Published: Sept. 5, 2024

Language: Английский

Citations

12
Functional innovation through new genes as a general evolutionary process DOI
Shengqian Xia, Jianhai Chen, Deanna Arsala

et al.

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

Language: Английский

Citations

1
Oncogenic signaling in the Drosophila prostate-like accessory gland activates a pro-tumorigenic program in the absence of proliferation DOI Creative Commons

Samuel Jaimian Church,

Ajai J. Pulianmackal,

Joseph A. Dixon

et al.

Disease Models & Mechanisms, Journal Year: 2025, Volume and Issue: 18(4)

Published: April 1, 2025

ABSTRACT Drosophila models for tumorigenesis have revealed conserved mechanisms of signaling involved in mammalian cancer. Many these use highly mitotically active tissues. Few adult tissues, when most cells are terminally differentiated and postmitotic. The accessory glands prostate-like a model prostate using this tissue has been explored. In prior model, oncogenic was induced during the proliferative stages gland development, raising question how activity impacts differentiated, postmitotic tissue. Here, we show that leads to activation pro-tumorigenic program, similar mitotic but absence proliferation. our experiments, led hypertrophy with nuclear anaplasia, part through endoreduplication. Oncogene-induced gene expression changes overlapped those polyploid cancer after chemotherapy, which potentially mediate tumor recurrence. Thus, provide useful aspects progression lack cellular

Language: Английский

Citations

0
Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins DOI Creative Commons
Eric B Zheng, Li Zhao

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Sept. 27, 2022

De novo gene origination, where a previously nongenic genomic sequence becomes genic through evolution, is increasingly recognized as an important source of novelty. Many de genes have been proposed to be protein-coding, and few experimentally shown yield protein products. However, the systematic study proteins has hampered by doubts regarding their translation without experimental observation Using systematic, mass-spectrometry-first computational approach, we identify 993 unannotated open reading frames with evidence (utORFs) in Drosophila melanogaster . To quantify similarity these utORFs across infer phylostratigraphic age, develop synteny-based approach. Combining results reference datasets ontissue- life stage-specific transcription conservation, different properties amongst utORFs. Contrary expectations, fastest-evolving are not youngest evolutionarily. We observed more brain than testis. Most identified may origin, even accounting for possibility false-negative detection. Finally, divergence after inferred origin event remains substantial, suggesting that turn over frequently. Our suggest there substantial unappreciated diversity evolution: many exist appreciated; divergent evolutionary trajectories, they gained lost All all, single characteristic model but instead, diverse trajectories.

Language: Английский

Citations

15
Single-nucleus transcriptomes reveal evolutionary and functional properties of cell types in theDrosophilaaccessory gland DOI Open Access

Alex C Majane,

Julie M. Cridland,

David J. Begun

et al.

Genetics, Journal Year: 2021, Volume and Issue: 220(2)

Published: Nov. 25, 2021

Abstract Many traits responsible for male reproduction evolve quickly, including gene expression phenotypes in germline and somatic reproductive tissues. Rapid evolution polyandrous species is thought to be driven by competition among males fertilizations conflicts between female fitness interests that manifest postcopulatory phenotypes. In Drosophila, seminal fluid proteins secreted three major cell types of the accessory gland ejaculatory duct are required sperm storage use, influence traits. Recent work has shown these have overlapping but distinct effects on biology, yet relatively little known about their evolutionary properties. Here, we use single-nucleus RNA-Seq from Drosophila melanogaster two closely related comprehensively describe diversity tissues transcriptome first time. We find transcripts strongly partitioned across types, many other genes additionally defines each type. also report previously undocumented main cells. Transcriptome divergence was found heterogeneous lineages, revealing a complex process. Furthermore, protein adaptation varied with potential consequences our understanding selection

Language: Английский

Citations

18
Identifying candidate de novo genes expressed in the somatic female reproductive tract of Drosophila melanogaster DOI Creative Commons

Kaelina D. Lombardo,

Hayley K. Sheehy,

Julie M. Cridland

et al.

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(8)

Published: June 1, 2023

Abstract Most eukaryotic genes have been vertically transmitted to the present from distant ancestors. However, variable gene number across species indicates that gain and loss also occurs. While new typically originate as products of duplications rearrangements preexisting genes, putative de novo genes—genes born out ancestrally nongenic sequence—have identified. Previous studies in Drosophila provided evidence expression male reproductive tissues is common. no focused on female tissues. Here we begin addressing this gap literature by analyzing transcriptomes 3 tract organs (spermatheca, seminal receptacle, parovaria) species—our focal species, melanogaster—and 2 closely related simulans yakuba, with goal identifying D. melanogaster-specific expressed these We discovered several candidate located sequence annotated intergenic. Consistent literature, tend be short, single exon, lowly expressed. find some are other melanogaster both sexes. The relatively small intergenic here similar observed accessory gland, but substantially fewer than testis.

Language: Английский

Citations

6
Male-derived transcripts isolated from the mated female reproductive tract in Drosophila melanogaster DOI Creative Commons

Julie M. Cridland,

David J. Begun

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(11)

Published: Sept. 19, 2023

In species with internal fertilization, sperm, and seminal fluid are transferred from male to female during mating. While both sperm contain various types of molecules, including RNA, the role most these molecules in coordination fertilization or other possible functions is poorly understood. Drosophila, exosomes accessory gland, which produces fluid, females, but their potential cargoes have not been described. Moreover, while RNA composition has described several mammalian species, little work on this problem occurred Drosophila. Here we use single nucleotide polymorphism differences between males females a set highly inbred lines D. melanogaster, transcriptome data reproductive tract, testis, investigate origin, vs female, isolated 3 tract organs, receptacle spermatheca, store parovaria, does not. We find that mated carry male-derived transcripts many genes, those markers gland known proteins. Our observations also support idea intact can be storage organs.

Language: Английский

Citations

6
Evolution of secondary cell number and position in the Drosophila accessory gland DOI Creative Commons
Yoko A. Takashima,

Alex C Majane,

David J. Begun

et al.

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(10), P. e0278811 - e0278811

Published: Oct. 25, 2023

In animals with internal fertilization, males transfer gametes and seminal fluid during copulation, both of which are required for successful reproduction. Drosophila other insects, is produced in the paired accessory gland (AG), ejaculatory duct, bulb. The D. melanogaster AG has emerged as an important model system this component male reproductive biology. Seminal proteins proper storage use sperm by females, also critical establishing maintaining a suite short- long-term postcopulatory female physiological responses that promote success. composed two main cell types. majority cells, referred to responsible production many proteins. A minority about 4%, secondary cells. These restricted distal tip AG, may play especially role maintenance post-mating response. Many studies evolution have suggested evolve quickly, does transcriptome. Here, we investigate number position collection eight species spanning entire history genus. We document heretofore underappreciated rapid evolutionary rate these specialized raising several questions developmental, functional, significance variation.

Language: Английский

Citations

6
Comprehensive Transcriptome Analysis in the Testis of the Silkworm, Bombyx mori DOI Creative Commons
Kohei Kakino, Hiroaki Mon,

Takeru Ebihara

et al.

Insects, Journal Year: 2023, Volume and Issue: 14(8), P. 684 - 684

Published: Aug. 2, 2023

Spermatogenesis is an important process in reproduction and conserved across species, but Bombyx mori, it shows peculiarities, such as the maintenance of spermatogonia by apical cells fertilization dimorphic spermatozoa. In this study, we attempted to characterize genes expressed testis B. focusing on aspects expression patterns gene function transcriptome comparisons between different tissues, internal regions, Drosophila melanogaster. The analysis 12 tissues including those testis, revealed widespread 20,962 1705 testis-specific genes. A comparative stem region (SR) differentiated regions (DR) 4554 3980 specific-enriched genes, respectively. addition, with D. melanogaster homologs 1204 SR 389 DR that were similarly equivalent testis. Moreover, ontology (GO) enrichment was performed for SR-specific enriched DR-specific GO terms several biological processes enriched, confirming previous findings. This study advances our understanding spermatogenesis mori provides basis future research, filling a knowledge gap fly mammalian studies.

Language: Английский

Citations

4
Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster DOI

Julie M. Cridland,

Colin E Contino,

David J. Begun

et al.

Genetics, Journal Year: 2023, Volume and Issue: 224(1)

Published: March 3, 2023

Abstract Transcriptome analysis of several animal clades suggests that male reproductive tract gene expression evolves quickly. However, the factors influencing abundance and distribution within-species variation, ultimate source interspecific divergence, are poorly known. Drosophila melanogaster, an ancestrally African species has recently spread throughout world colonized Americas in last roughly 100 years, exhibits phenotypic genetic latitudinal clines on multiple continents, consistent with a role for spatially varying selection shaping its biology. Nevertheless, geographic variation is described, as relationship to variation. Here, we investigate these issues through two tissue transcriptomes [testis accessory gland (AG)] samples from Maine (USA), Panama, Zambia. We find dramatic differences between tissues differential glands exhibiting abundant differentiation testis very little. Latitudinal appears be influenced by Panama phenotypes. While shows little differentiation, it much greater than Zambia vs American population comparisons. Expression both non-randomly distributed across genome chromosome arm scale. Interspecific divergence D. melanogaster simulans discordant rates populations. Strongly heterogeneous timescales complex evolutionary process involving major temporal changes way influences evolution organs.

Language: Английский

Citations

3