scholarly journals The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kevin Kit Siong Ng ◽  
Masaki J. Kobayashi ◽  
Jeffrey A. Fawcett ◽  
Masaomi Hatakeyama ◽  
Timothy Paape ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Irrigation Treatment ◽  
Tropical Trees ◽  
Molecular Dating ◽  
Annual Rainfall ◽  
Tropical Rainforests ◽  
Comparative Genomic ◽  
Ecological Studies ◽  
Extinction Event ◽  
Shorea Leprosula

AbstractHyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.

scholarly journals The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications

2014 ◽  
Author(s):  
Jeramiah Smith
Keyword(s):  
Genome Duplication ◽  
Strong Support ◽  
Sea Lamprey ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Segmental Duplications ◽  
Vertebrate Genome ◽  
Vertebrate Lineage ◽  
Comparative Maps ◽  
Genome Duplications

Gene and genome duplications serve as an important reservoir of material for the evolution of new biological functions. It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey, a representative of an ancient lineage that diverged from all other vertebrates approximately 550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1N ~ 99), spanning a total of 5,570.25 cM. Comparative mapping data yield strong support for one ancient whole genome duplication but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionary independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations into the evolution of vertebrate gene functions.

scholarly journals Ecological studies of polyploidy in the 100 years following its discovery

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130352 ◽  
Author(s):  
Justin Ramsey ◽  
Tara S. Ramsey
Keyword(s):  
Species Interactions ◽  
Life History Traits ◽  
Genome Duplication ◽  
Crop Improvement ◽  
Plant Ecology ◽  
Ecological Context ◽  
Ecological Studies ◽  
Phenotypic Differences ◽  
Cytogenetic Studies

Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions—as achieved from divergence of physiological and life-history traits—but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910s–1930s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930s–1950s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940s and 1950s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se . The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s–1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy—regarded by most botanists as the primary mode of genome duplication—is largely unstudied in an ecological context.

scholarly journals Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yifei Liu ◽  
Bo Wang ◽  
Shaohua Shu ◽  
Zheng Li ◽  
Chi Song ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Coptis Chinensis ◽  
Phylogenetic Placement ◽  
Genomic Landscape ◽  
Genomic Analyses ◽  
Early Diverging Eudicots ◽  
Functional Versatility ◽  
Tandem Duplications

AbstractChinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.

scholarly journals Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhang ◽  
Yan Wang ◽  
Tao Chen ◽  
Qing Chen ◽  
Lei Wang ◽  
...  
Keyword(s):  
Single Copy ◽  
Genomic Variation ◽  
Molecular Dating ◽  
Divergent Evolution ◽  
Comparative Genomic ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Longmenshan Fault ◽  
Plastid Protein ◽  
Phylogenomic Analyses

Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including Cerasus (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives.

scholarly journals Assessing the Australian Termite Diversity Anomaly: How Habitat and Rainfall Affect Termite Assemblages

2021 ◽  
Vol 9 ◽  
Author(s):  
Rebecca A. Clement ◽  
Habacuc Flores-Moreno ◽  
Lucas A. Cernusak ◽  
Alexander W. Cheesman ◽  
Abbey R. Yatsko ◽  
...  
Keyword(s):  
Dead Wood ◽  
Annual Rainfall ◽  
Tropical Rainforests ◽  
Termite Species ◽  
Tropical Regions ◽  
Feeding Groups ◽  
Feeding Group ◽  
Grass Litter ◽  
High Precipitation ◽  
Group Diversity

Termites are important ecosystem engineers in tropical habitats, with different feeding groups able to decompose wood, grass, litter, and soil organic matter. In most tropical regions, termite abundance and species diversity are assumed to increase with rainfall, with highest levels found in rainforests. However, in the Australian tropics, this pattern is thought to be reversed, with lower species richness and termite abundance found in rainforest than drier habitats. The potential mechanisms underlying this pattern remain unclear. We compared termite assemblages (abundance, activity, diversity, and feeding group composition) across five sites along a precipitation gradient (ranging from ∼800 to 4,000 mm annual rainfall), spanning dry and wet savanna habitats, wet sclerophyll, and lowland and upland rainforests in tropical North Queensland. Moving from dry to wet habitats, we observed dramatic decreases in termite abundance in both mounds and dead wood occupancy, with greater abundance and activity at savanna sites (low precipitation) compared with rainforest or sclerophyll sites (high precipitation). We also observed a turnover in termite species and feeding group diversity across sites that were close together, but in different habitats. Termite species and feeding group richness were highest in savanna sites, with 13 termite species from wood-, litter-, grass-, dung-, and soil-feeding groups, while only five termite species were encountered in rainforest and wet sclerophyll sites—all wood feeders. These results suggest that the Australian termite diversity anomaly may be partly driven by how specific feeding groups colonized habitats across Australia. Consequently, termites in Australian rainforests may be less important in ecosystem processes, such as carbon and nutrient cycling during decomposition, compared with termites in other tropical rainforests.

scholarly journals The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6320 ◽  
Author(s):  
Zhen Yang ◽  
Guixi Wang ◽  
Qinghua Ma ◽  
Wenxu Ma ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Molecular Dating ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Genome Variation ◽  
Genome Data ◽  
Chloroplast Genomes

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

scholarly journals The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

2020 ◽  
Author(s):  
ERIK J M Koenen ◽  
Dario I Ojeda ◽  
Freek T Bakker ◽  
Jan J Wieringa ◽  
Catherine Kidner ◽  
...  
Keyword(s):  
Mass Extinction ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Tree ◽  
Early Evolution ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Extinction Event ◽  
Mass Extinction Event ◽  
Gene Tree Reconciliation

Abstract The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]

scholarly journals A series of terribly unfortunate events: How environment and infection synergized to cause the Kihansi spray toad extinction

2021 ◽  
Author(s):  
Thomas R Sewell ◽  
Lucy van Dorp ◽  
Pria Ghosh ◽  
Claudia Wierzbicki ◽  
Cristian Caroe ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Batrachochytrium Dendrobatidis ◽  
Abiotic Factors ◽  
Emerging Infectious Diseases ◽  
Molecular Dating ◽  
Habitat Modification ◽  
Mountainous Region ◽  
Extinction Event ◽  
Negative Impacts ◽  
Kihansi Spray Toad

Outbreaks of emerging infectious diseases are trained by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Extinction of the Tanzanian Kihansi spray toad (Nectophrynoides asperginis) in 2004 was contemporaneous with the construction of a dam, implicating habitat modification in the loss of this species. However, high burdens of a globally emerging infection, Batrachochytrium dendrobatidis (Bd) were synchronously observed implicating infectious disease in this toads extinction. Here, by shotgun sequencing skin DNA from archived toad mortalities and assembling chytrid mitogenomes, we prove this outbreak was caused by the BdCAPE lineage and not the panzootic lineage BdGPL that is widely associated with global amphibian extinctions. Molecular dating showed an invasion of BdCAPE across Southern Africa overlapping with the timing of the extinction event. However, post-outbreak surveillance of conspecific species inhabiting this mountainous region showed widespread infection by BdCAPE yet no signs of amphibian ill-health or species decline. Our findings show that despite efforts to mitigate the environmental impact caused by dams construction, invasion of the pathogen ultimately led to the loss of the Kihansi spray toad; a synergism between emerging infectious disease and environmental change that likely heralds wider negative impacts on biodiversity in the Anthropocene.

scholarly journals An ancient genome duplication in the speciose reef-building coral genus, Acropora

2018 ◽  
Author(s):  
Yafei Mao ◽  
Chuya Shinzato ◽  
Noriyuki Satoh
Keyword(s):  
Stress Responses ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Duplicated Genes ◽  
Most Recent Common Ancestor ◽  
Coral Genus ◽  
Evolutionary Force ◽  
Regulation Functions

AbstractWhole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of vertebrates, plants, and other organisms. Acropora, one of the most speciose reef-building coral genera, responsible for creating spectacular but increasingly threatened marine ecosystems, is suspected to have originated by polyploidy, yet there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed five Acropora genomes and an Astreopora genome (Scleractinia: Acroporidae) to show that a WGD event likely occurred between 27.9 and 35.7 Million years ago (Mya) in the most recent common ancestor of Acropora, concurrent with a massive worldwide coral extinction. We found that duplicated genes became highly enriched in gene regulation functions, some of which are involved in stress responses. The different functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some gene duplications of proteinaceous toxins were generated by WGD in Acropora compared with other Cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals and it helps to explain the origin and diversification of Acropora.

scholarly journals Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes

2018 ◽  
Author(s):  
Yan Wang ◽  
Noha Youssef ◽  
M.B. Couger ◽  
Radwa Hanafy ◽  
Mostafa Elshahed ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Molecular Dating ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Gene Gain ◽  
Plant Materials ◽  
Most Recent Common Ancestor ◽  
The Impact ◽  
Lineage Specific Genes

AbstractThe anaerobic gut fungi (AGF) or Neocallimastigomycota inhabit the rumen and alimentary tract of herbivorous mammals, where they play an important role in the degradation of plant fiber. Comparative genomic and phylogenomic analysis of the AGF has long been hampered by their fastidious growth pattern as well as their large and AT-biased genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available genome sequences of AGF taxa to explore their evolutionary relationships, time their divergence, and characterize patterns of gene gain/loss associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a timeframe that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of these independently estimated ages of AGF evolution, grasses evolution, and mammalian transition to herbivory suggest that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes and protein domains in the AGF, two of which were acquired from an animal host (galectin) and rumen gut bacteria (carbohydrate-binding domain) via horizontal gene transfer (HGT). Four of the bacterial derived “Cthe_2159” genes in AGF genomes also encode eukaryotic Pfam domains (“Atrophin-1”, “eIF-3_zeta”, “Nop14”, and “TPH”) indicating possible gene fusion events after the acquisition of “Cthe_2159” domain. A third AGF domain, plant-like polysaccharide lyase N-terminal domain (“Rhamnogal_lyase”), represents the first report from fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed the presence and expression of these lineage-specific genes in nearly all AGF clades supporting the hypothesis that these laterally acquired and novel genes in fungi are likely functional. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.

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