Unbiased subgenome evolution in allotetraploid species of Ephedra and its implications for the evolution of large genomes in gymnosperms

Abstract The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data. We found that the two subgenomes of the allotetraploids had similar numbers of expressed homeologs, similar percentages of homeologs with dominant expression, and approximately equal numbers of isoforms with alternative splicing, showing an unbiased subgenome evolution as in a few polyploid angiosperms, with a divergence of the two subgenomes at approximately 8 Mya. In addition, the nuclear DNA content of the allotetraploid species is almost equal to the sum of two putative progenitors, suggesting limited genome restructuring after allotetraploid speciation. The allopolyploid species of Ephedra might have undergone slow diploidization, and the unbiased subgenome evolution implies that the formation of large genomes in gymnosperms could be attributed to even and slow fractionation following polyploidization.

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Genome Sizes in Hepatica Mill: (Ranunculaceae) Show a Loss of DNA, Not a Gain, in Polyploids

Journal of Botany ◽

10.1155/2010/758260 ◽

2010 ◽

Vol 2010 ◽

pp. 1-7 ◽

Cited By ~ 7

Author(s):

B. J. M. Zonneveld

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Close Relationships ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Dna Contents ◽

Asiatic Species ◽

Nuclear Dna Contents ◽

Allotetraploid Species

Genome size (C-value) was applied anew to investigate the relationships within the genus Hepatica (Ranunculaceae). More than 50 samples representing all species (except H. falconeri), from wild and cultivated material, were investigated. Species of Hepatica turn out to be diploid (), tetraploid ( ), and a possible pentaploid. The somatic nuclear DNA contents (2C-value), as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14%) loss of nuclear DNA in the natural allopolyploids was found.

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Prognostic value of nuclear DNA content in papillary and follicular thyroid cancer

World Journal of Surgery ◽

10.1007/bf01655433 ◽

1988 ◽

Vol 12 (4) ◽

pp. 503-507 ◽

Cited By ~ 29

Author(s):

Jaap F. Hamming ◽

Lodewijk J. D. M. Schelfhout ◽

Cees J. Cornelisse ◽

Cornelis J. H. van de Velde ◽

Bernard M. Goslings ◽

...

Keyword(s):

Thyroid Cancer ◽

Dna Content ◽

Prognostic Value ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Follicular Thyroid Cancer

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Nuclei isolation protocols for flow cytometry allowing nuclear DNA content estimation in problematic microalgal groups

Journal of Applied Phycology ◽

10.1007/s10811-021-02433-z ◽

2021 ◽

Author(s):

Dora Čertnerová

Keyword(s):

Flow Cytometry ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Nuclei Isolation

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Sequential production of gametes during meiosis in trypanosomes

Communications Biology ◽

10.1038/s42003-021-02058-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Lori Peacock ◽

Chris Kay ◽

Chloe Farren ◽

Mick Bailey ◽

Mark Carrington ◽

...

Keyword(s):

Salivary Glands ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Cell Types ◽

Tsetse Fly ◽

Binucleate Cell ◽

Insect Vector ◽

Content Ratio ◽

Different Cell Types ◽

Meiosis I

AbstractMeiosis is a core feature of eukaryotes that occurs in all major groups, including the early diverging excavates. In this group, meiosis and production of haploid gametes have been described in the pathogenic protist, Trypanosoma brucei, and mating occurs in the salivary glands of the insect vector, the tsetse fly. Here, we searched for intermediate meiotic stages among trypanosomes from tsetse salivary glands. Many different cell types were recovered, including trypanosomes in Meiosis I and gametes. Significantly, we found trypanosomes containing three nuclei with a 1:2:1 ratio of DNA contents. Some of these cells were undergoing cytokinesis, yielding a mononucleate gamete and a binucleate cell with a nuclear DNA content ratio of 1:2. This cell subsequently produced three more gametes in two further rounds of division. Expression of the cell fusion protein HAP2 (GCS1) was not confined to gametes, but also extended to meiotic intermediates. We propose a model whereby the two nuclei resulting from Meiosis I undergo asynchronous Meiosis II divisions with sequential production of haploid gametes.

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Estimation of nuclear DNA content by flow cytometry in fishes of the genus Xiphophorus

Comparative Biochemistry and Physiology Part B Comparative Biochemistry ◽

10.1016/0305-0491(89)90182-x ◽

1989 ◽

Vol 94 (3) ◽

pp. 465-468 ◽

Cited By ~ 14

Author(s):

Terrence R. Tiersch ◽

Robert W. Chandler ◽

Klaus D. Kallman ◽

Stephen S. Wachtel

Keyword(s):

Flow Cytometry ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content

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Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)

Genes ◽

10.3390/genes12060896 ◽

2021 ◽

Vol 12 (6) ◽

pp. 896

Author(s):

Yuenan Zhou ◽

Pei Yang ◽

Shuang Xie ◽

Min Shi ◽

Jianhua Huang ◽

...

Keyword(s):

Alternative Splicing ◽

Adult Development ◽

Sexual Development ◽

Molecular Mechanisms ◽

Parasitic Wasp ◽

Differentially Expressed Gene ◽

Regulation Mechanism ◽

Rna Seq ◽

Male And Female ◽

Cotesia Vestalis

The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.

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Characterization of alternative splicing events and prognostic signatures in breast cancer

BMC Cancer ◽

10.1186/s12885-021-08305-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Pihua Han ◽

Jingjun Zhu ◽

Guang Feng ◽

Zizhang Wang ◽

Yanni Ding

Keyword(s):

Breast Cancer ◽

Alternative Splicing ◽

Proportional Hazards ◽

Pearson Correlation ◽

Original Data ◽

Cox Proportional Hazards ◽

Prognostic Indicators ◽

Splicing Factors ◽

Rna Seq

Abstract Background Breast cancer (BRCA) is one of the most common cancers worldwide. Abnormal alternative splicing (AS) frequently observed in cancers. This study aims to demonstrate AS events and signatures that might serve as prognostic indicators for BRCA. Methods Original data for all seven types of splice events were obtained from TCGA SpliceSeq database. RNA-seq and clinical data of BRCA cohorts were downloaded from TCGA database. Survival-associated AS events in BRCA were analyzed by univariate COX proportional hazards regression model. Prognostic signatures were constructed for prognosis prediction in patients with BRCA based on survival-associated AS events. Pearson correlation analysis was performed to measure the correlation between the expression of splicing factors (SFs) and the percent spliced in (PSI) values of AS events. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to demonstrate pathways in which survival-associated AS event is enriched. Results A total of 45,421 AS events in 21,232 genes were identified. Among them, 1121 AS events in 931 genes significantly correlated with survival for BRCA. The established AS prognostic signatures of seven types could accurately predict BRCA prognosis. The comprehensive AS signature could serve as independent prognostic factor for BRCA. A SF-AS regulatory network was therefore established based on the correlation between the expression levels of SFs and PSI values of AS events. Conclusions This study revealed survival-associated AS events and signatures that may help predict the survival outcomes of patients with BRCA. Additionally, the constructed SF-AS networks in BRCA can reveal the underlying regulatory mechanisms in BRCA.

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