scholarly journals Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates

2020 ◽  
Vol 21 (24) ◽  
pp. 9562
Author(s):  
Mikhail V. Fofanov ◽  
Dmitry Yu. Prokopov ◽  
Heiner Kuhl ◽  
Manfred Schartl ◽  
Vladimir A. Trifonov
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Profiles ◽  
Single Copy ◽  
Protein Product ◽  
Whole Genome ◽  
Acipenser Ruthenus ◽  
Microrna Processing ◽  
Additional Segment ◽  
Sterlet Acipenser Ruthenus

MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.

scholarly journals Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor (ARF) Genes in Foxtail Millet (Setaria italica L.)

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
You Chen ◽  
Bin Liu ◽  
Yujun Zhao ◽  
Wenzhe Yu ◽  
Weina Si
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Profiles ◽  
Foxtail Millet ◽  
Purifying Selection ◽  
Functional Redundancy ◽  
Setaria Italica ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Auxin Response

Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of ARF genes was seldom investigated in Setaria italica, an important crop and C4 model plant. In the present study, genome-wide evolutionary analysis of ARFs was performed in S. italica. Twenty-four SiARF genes were identified and unevenly distributed on eight of the nine chromosomes in S. italica. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of SiARFs under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of SiARFs and benefit for further functional characterization.

scholarly journals Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)

2020 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Doubling ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested a series of scenarios describing different polyploidization events.Results: Using target sequence capture, we generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. Species of Hibiscus shared one genome duplication with H. syriacus and one whole genome duplication occurred along the branch leading to H. syriacus.Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages and chelicerate genome architecture

2021 ◽  
Author(s):  
Guilherme Gainett ◽  
Vanessa L. González ◽  
Jesús A. Ballesteros ◽  
Emily V. W. Setton ◽  
Caitlin M. Baker ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Hox Genes ◽  
Genome Duplication ◽  
Draft Genome ◽  
Growth Factor Receptor ◽  
Single Copy ◽  
Developmental Genetics ◽  
Genome Architecture ◽  
Whole Genome ◽  
Duplication Events

AbstractChelicerates exhibit dynamic evolution of genome architecture, with multiple whole genome duplication events affecting groups like spiders, scorpions, and horseshoe crabs. Yet, genomes remain unavailable for several chelicerate orders, such as Opiliones (harvestmen), which has hindered comparative genomics and developmental genetics across arachnids. We assembled a draft genome of the daddy-long-legs Phalangium opilio, which revealed no signal of whole genome duplication. To test the hypothesis that single-copy Hox genes of the harvestman exhibit broader functions than subfunctionalized spider paralogs, we performed RNA interference against Deformed in P. opilio. Knockdown of Deformed incurred homeotic transformation of the two anterior pairs of walking legs into pedipalpal identity; by comparison, knockdown of the spatially restricted paralog Deformed-A in the spider affects only the first walking leg. To investigate the genetic basis for leg elongation and tarsomere patterning, we identified and interrogated the function of an Epidermal growth factor receptor (Egfr) homolog. Knockdown of Egfr incurred shortened appendages and the loss of distal leg structures. The overlapping phenotypic spectra of Egfr knockdown experiments in the harvestman and multiple insect models are striking because tarsomeres have evolved independently in these groups. Our results suggest a conserved role for Egfr in patterning distal leg structures across arthropods, as well as cooption of EGFR signaling in tarsomere patterning in both insects and arachnids. The establishment of genomic resources for P. opilio, together with functional investigations of appendage fate specification and distal patterning mechanisms, are key steps in understanding how daddy-long-legs make their long legs.

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
J. S. Eriksson ◽  
C. D. Bacon ◽  
D. J. Bennett ◽  
B. E. Pfeil ◽  
B. Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

2015 ◽  
Vol 112 (48) ◽  
pp. 14918-14923 ◽  
Author(s):  
Jun Inoue ◽  
Yukuto Sato ◽  
Robert Sinclair ◽  
Katsumi Tsukamoto ◽  
Mutsumi Nishida
Keyword(s):  
Mathematical Modeling ◽  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Single Copy ◽  
Marker Genes ◽  
Whole Genome ◽  
Protein Coding ◽  
Evolutionary Innovation

Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post–teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70–80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.

GENE LOSS UNDER NEIGHBORHOOD SELECTION FOLLOWING WHOLE GENOME DUPLICATION AND THE RECONSTRUCTION OF THE ANCESTRAL POPULUS GENOME

2009 ◽  
Vol 07 (03) ◽  
pp. 499-520 ◽  
Author(s):  
CHUNFANG ZHENG ◽  
P. KERR WALL ◽  
JAMES LEEBENS-MACK ◽  
CLAUDE DE PAMPHILIS ◽  
VICTOR A. ALBERT ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Chromosome Doubling ◽  
Populus Trichocarpa ◽  
Single Copy ◽  
Whole Genome ◽  
Gene Sets ◽  
Large Numbers ◽  
Neighborhood Selection

We develop criteria to detect neighborhood selection effects on gene loss following whole genome duplication, and apply them to the recently sequenced poplar (Populus trichocarpa) genome. We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the poplar and grapevine (Vitis vinifera) genomes, as T and R respectively. We conclude that, after chromosome doubling, the "choice" of which paralogous gene pairs will lose copies is random, but that the retention of strings of single-copy genes on one chromosome versus the other is decidedly non-random.

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