scholarly journals Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses

2019 ◽  
Author(s):  
Bei Gao ◽  
Moxian Chen ◽  
Xiaoshuang Li ◽  
Yuqing Liang ◽  
Daoyuan Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Physcomitrella Patens ◽  
Duplication Event ◽  
Land Plant ◽  
Phylogenetic Position ◽  
List Type ◽  
Genome Duplication Event ◽  
Genome Duplications ◽  
Duplication Events ◽  
Phylogenomic Analyses

SummaryMosses (Bryophyta) are a key group occupying important phylogenetic position for understanding land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage and contains more than 95% of the modern mosses, whereas the other classes are by nature species-poor. The phylogeny of mosses remains elusive at present.Recurrent whole genome duplications have shaped the evolution trajectory of angiosperms, but little is known about the genome evolutionary history in mosses. It remains to be answered if there existed a historical genome duplication event associated with the species radiation of class Bryopsida.Here, the high-confidence moss phylogeny was generated covering major moss lineages. Two episodes of ancient genomic duplication events were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida and Tetraphidopsida, with estimated ages of the gene duplications clustered around 329 and 182 million year ago, respectively.The third episode of polyploidy event (termed ψ) was tightly associated with the early diversification of Bryopsida with an estimated age of ~87 million years. By scrutinizing the phylogenetic timing of duplicated syntelogs in Physcomitrella patens, the WGD1 and WGD2 events were confidently re-recognized as the ψ event and the Funarioideae duplication event (~65 mya), respectively. Together, our findings unveiled four episodes of polyploidy events in the evolutionary past of Physcomitrella patens.

scholarly journals Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1375
Author(s):  
Larisa S. Biltueva ◽  
Dmitry Yu. Prokopov ◽  
Svetlana A. Romanenko ◽  
Elena A. Interesova ◽  
Manfred Schartl ◽  
...  
Keyword(s):  
Duplication Event ◽  
Siberian Sturgeon ◽  
Genome Duplication Event ◽  
Acipenser Baerii ◽  
Whole Genome Duplications ◽  
Sturgeon Species ◽  
Genome Duplications ◽  
Size Groups ◽  
Genomic Studies ◽  
Syntenic Regions

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

scholarly journals Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

2017 ◽  
Author(s):  
Alex B. Brohammer ◽  
Thomas JY. Kono ◽  
Nathan M. Springer ◽  
Suzanne E. McGaugh ◽  
Candice N. Hirsch
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Duplicate Gene ◽  
Duplication Event ◽  
Inbred Lines ◽  
Whole Genome ◽  
Ancestral State ◽  
Genome Duplication Event ◽  
Number Variation ◽  
And Function

SUMMARYMaize is a diverse paleotetraploid species with widespread presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization and differential fractionation refers to non-shared gene loss events between individuals. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variable syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable compared to syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.SIGNIFICANCE STATEMENTThere is a large amount of presence/absence variation for gene content in maize. One mechanism that has been hypothesized to contribute to this variation is differential fractionation between individuals following the maize whole genome duplication event. Using comparative genomics, with sorghum and rice representing the ancestral state, we observed little evidence of differential fractionation among elite inbred lines and the few differentially fractionated genes identified did not appear to confer functional significance.

scholarly journals Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

2019 ◽  
Vol 37 (3) ◽  
pp. 730-756 ◽  
Author(s):  
Irene Julca ◽  
Marina Marcet-Houben ◽  
Fernando Cruz ◽  
Carlos Vargas-Chavez ◽  
John Spencer Johnston ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Duplication Event ◽  
Aphid Species ◽  
Common Finding ◽  
Segmental Duplications ◽  
Genome Duplication Event ◽  
Phloem Sap ◽  
Recent Species ◽  
Species Specific

Abstract Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

scholarly journals A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Zheng Fan ◽  
Tao Yuan ◽  
Piao Liu ◽  
Lu-Yu Wang ◽  
Jian-Feng Jin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Duplication Event ◽  
Whole Genome ◽  
High Quality ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Chromosome Level

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

scholarly journals Axenic in-vitro cultivation of nineteen peat-moss (Sphagnum L.) species as a resource for basic biology, biotechnology and paludiculture

2020 ◽  
Author(s):  
Melanie A. Heck ◽  
Volker M. Lüth ◽  
Matthias Krebs ◽  
Mira Kohl ◽  
Anja Prager ◽  
...  
Keyword(s):  
Large Scale ◽  
Physcomitrella Patens ◽  
Peat Moss ◽  
In Vitro Cultivation ◽  
List Type ◽  
High Quality ◽  
Renewable Biomass ◽  
Basic Biology ◽  
Axenic Cultivation

SummaryThe cultivation of Sphagnum mosses reduces CO2 emissions by rewetting drained peatlands and by substituting peat with renewable biomass. ‘Sphagnum farming’ requires large volumes of founder material, which can only be supplied sustainably by axenic cultivation in bioreactors.We established axenic in-vitro cultures from sporophytes of 19 Sphagnum species collected in Austria, Germany, Latvia, Netherlands, Russia and Sweden, namely S. angustifolium, S. balticum, S. capillifolium, S. centrale, S. compactum, S. cuspidatum, S. fallax, S. fimbriatum, S. fuscum, S. lindbergii, S. medium/divinum, S. palustre, S. papillosum, S. rubellum, S. russowii, S. squarrosum, S. subnitens, S. subfulvum, and S. warnstorfii. These species cover five of the six European Sphagnum sections, namely Acutifolia, Cuspidata, Rigida, Sphagnum and Squarrosa.Their growth was measured in axenic suspension cultures, whereas their ploidy was determined by flow cytometry and compared with the genome size of Physcomitrella patens. We identified haploid and diploid Sphagnum species, found that their cells are predominantly arrested in the G1-phase of the cell cycle, and did not find a correlation between plant productivity and ploidy.With this collection, high-quality founder material for diverse large-scale applications but also for basic Sphagnum research is available from the International Moss Stock Center (IMSC).

scholarly journals The water lily genome and the early evolution of flowering plants

Nature ◽  
2019 ◽  
Vol 577 (7788) ◽  
pp. 79-84 ◽  
Author(s):  
Liangsheng Zhang ◽  
Fei Chen ◽  
Xingtan Zhang ◽  
Zhen Li ◽  
Yiyong Zhao ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Early Evolution ◽  
Phylogenetic Position ◽  
Whole Genome ◽  
Biosynthetic Genes ◽  
Genome Duplication Event ◽  
Water Lily ◽  
Floral Scents

AbstractWater lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.

scholarly journals Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130353 ◽  
Author(s):  
Kevin Vanneste ◽  
Steven Maere ◽  
Yves Van de Peer
Keyword(s):  
Large Scale ◽  
Plant Evolution ◽  
Small Scale ◽  
Whole Genome ◽  
Polyploid Species ◽  
Plant Genomes ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Duplication Events ◽  
Biological Innovations

Genome sequencing has demonstrated that besides frequent small-scale duplications, large-scale duplication events such as whole genome duplications (WGDs) are found on many branches of the evolutionary tree of life. Especially in the plant lineage, there is evidence for recurrent WGDs, and the ancestor of all angiosperms was in fact most likely a polyploid species. The number of WGDs found in sequenced plant genomes allows us to investigate questions about the roles of WGDs that were hitherto impossible to address. An intriguing observation is that many plant WGDs seem associated with periods of increased environmental stress and/or fluctuations, a trend that is evident for both present-day polyploids and palaeopolyploids formed around the Cretaceous–Palaeogene (K–Pg) extinction at 66 Ma. Here, we revisit the WGDs in plants that mark the K–Pg boundary, and discuss some specific examples of biological innovations and/or diversifications that may be linked to these WGDs. We review evidence for the processes that could have contributed to increased polyploid establishment at the K–Pg boundary, and discuss the implications on subsequent plant evolution in the Cenozoic.

scholarly journals Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

2020 ◽  
Vol 287 (1934) ◽  
pp. 20201538
Author(s):  
Euki Yazaki ◽  
Keitaro Kume ◽  
Takashi Shiratori ◽  
Yana Eglit ◽  
Goro Tanifuji ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Phylogenetic Position ◽  
Acetyl Coa ◽  
Transcriptomic Data ◽  
Substrate Level Phosphorylation ◽  
Substrate Level ◽  
Phylogenomic Analyses

We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected a putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.

scholarly journals Diversification of Non-TIR Class NB-LRR Genes in Relation to Whole-Genome Duplication Events in Arabidopsis

2005 ◽  
Vol 18 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Kan Nobuta ◽  
Tom Ashfield ◽  
Sun Kim ◽  
Roger W. Innes
Keyword(s):  
Segmental Duplication ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Phylogenetic Analyses ◽  
Synonymous Substitution ◽  
Duplication Event ◽  
Whole Genome ◽  
R Genes ◽  
Genome Duplication Event ◽  
Duplication Events

Arabidopsis thaliana is believed to have experienced at least two and possibly three whole-genome duplication events in its evolutionary history. In order to investigate the evolutionary relationships between these duplication events and diversification of disease resistance (R) genes, segmental-duplication events containing R genes belonging to the nucleotide binding-leucine rich repeat (NB-LRR) class were identified. Of 153 segmental-duplication events containing NB-LRR genes, only 22 contained NB-LRR genes in both members of the duplication pair, indicating a high frequency of NB-LRR gene loss after wholegenome duplication. The relative age of the duplication events was estimated based on the average synonymous substitution rate of the duplicated gene pairs in the segments. These data were combined with phylogenetic analyses. NB-LRR genes present in segment pairs derived from the most recent whole-genome duplication event, estimated to have occurred only 20 to 40 million years ago, occupy very distant branches of the NB-LRR phylogenetic tree. These data suggest that when NB-LRR clusters are duplicated as part of a whole-genome duplication, homoeologous NB-LRR genes are preferentially lost, either by eliminating one copy of the cluster or by eliminating individual genes such that only paralogous NB-LRR genes are maintained.

scholarly journals A new time-scale for ray-finned fish evolution

2006 ◽  
Vol 274 (1609) ◽  
pp. 489-498 ◽  
Author(s):  
Imogen A Hurley ◽  
Rachel Lockridge Mueller ◽  
Katherine A Dunn ◽  
Eric J Schmidt ◽  
Matt Friedman ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Nuclear Data ◽  
Duplication Event ◽  
Molecular Data ◽  
Morphological Data ◽  
Crown Group ◽  
Genome Duplication Event ◽  
Evolutionary Origins ◽  
Date Estimate

The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.

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