scholarly journals Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

2020 ◽  
Author(s):  
Cheng Sun ◽  
Jiaxing Huang ◽  
Yun Wang ◽  
Xiaomeng Zhao ◽  
Long Su ◽  
...  
Keyword(s):  
Social Evolution ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Repetitive Sequences ◽  
Gene Tree ◽  
Pathogen Transmission ◽  
Genomic Variation ◽  
Social Parasite ◽  
Behavioral Traits

AbstractBumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary lifecycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. These high-quality genomic resources capture natural genetic and phenotypic variation across bumblebees, offering new opportunities to advance our understanding of their remarkable ecological success and to identify and manage current and future threats.

scholarly journals Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

2020 ◽  
Author(s):  
Cheng Sun ◽  
Jiaxing Huang ◽  
Yun Wang ◽  
Xiaomeng Zhao ◽  
Long Su ◽  
...  
Keyword(s):  
Social Evolution ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Repetitive Sequences ◽  
Gene Tree ◽  
Pathogen Transmission ◽  
Genomic Variation ◽  
Social Parasite ◽  
Behavioral Traits

Abstract Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.

scholarly journals Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

2017 ◽  
Author(s):  
Meng Wu ◽  
Jamie L. Kostyun ◽  
Matthew W. Hahn ◽  
Leonie Moyle
Keyword(s):  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Fruit Color ◽  
Species Tree ◽  
Color Variation ◽  
Lineage Sorting ◽  
Floral Character ◽  
Trait Evolution

ABSTRACTPhylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and several introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.

scholarly journals Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

2018 ◽  
Author(s):  
M Rouard ◽  
G Droc ◽  
G Martin ◽  
J Sardos ◽  
Y Hueber ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Families ◽  
Musa Acuminata ◽  
Specific Gene ◽  
Rapid Radiation ◽  
High Sequence Identity ◽  
Short Period

AbstractEdible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships and genome evolution. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across a substantial portion of the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support future evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.

scholarly journals The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Flowering Plant ◽  
Estimation Methods ◽  
Lineage Sorting ◽  
Tree Estimation ◽  
Perfect Storm

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

2021 ◽  
Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Chromosome Conformation ◽  
Important Species

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.

scholarly journals How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

2022 ◽  
Vol 12 ◽  
Author(s):  
Martha Kandziora ◽  
Petr Sklenář ◽  
Filip Kolář ◽  
Roswitha Schmickl
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Secondary Contact ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Phylogenetic Discordance ◽  
Gene Tree Discordance ◽  
High Degree

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

scholarly journals Vectored Immunotherapeutics for Infectious Diseases: Can rAAVs Be The Game Changers for Fighting Transmissible Pathogens?

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhan ◽  
Manish Muhuri ◽  
Phillip W. L. Tai ◽  
Guangping Gao
Keyword(s):  
Infectious Diseases ◽  
Neutralizing Antibodies ◽  
Viral Vectors ◽  
De Novo ◽  
Genomic Variation ◽  
Transduction Efficiency ◽  
Foreign Proteins ◽  
Repeated Dosing

Conventional vaccinations and immunotherapies have encountered major roadblocks in preventing infectious diseases like HIV, influenza, and malaria. These challenges are due to the high genomic variation and immunomodulatory mechanisms inherent to these diseases. Passive transfer of broadly neutralizing antibodies may offer partial protection, but these treatments require repeated dosing. Some recombinant viral vectors, such as those based on lentiviruses and adeno-associated viruses (AAVs), can confer long-term transgene expression in the host after a single dose. Particularly, recombinant (r)AAVs have emerged as favorable vectors, given their high in vivo transduction efficiency, proven clinical efficacy, and low immunogenicity profiles. Hence, rAAVs are being explored to deliver recombinant antibodies to confer immunity against infections or to diminish the severity of disease. When used as a vaccination vector for the delivery of antigens, rAAVs enable de novo synthesis of foreign proteins with the conformation and topology that resemble those of natural pathogens. However, technical hurdles like pre-existing immunity to the rAAV capsid and production of anti-drug antibodies can reduce the efficacy of rAAV-vectored immunotherapies. This review summarizes rAAV-based prophylactic and therapeutic strategies developed against infectious diseases that are currently being tested in pre-clinical and clinical studies. Technical challenges and potential solutions will also be discussed.

scholarly journals ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter

2016 ◽  
Author(s):  
Shaun D Jackman ◽  
Benjamin P Vandervalk ◽  
Hamid Mohamadi ◽  
Justin Chu ◽  
Sarah Yeo ◽  
...  
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Message Passing ◽  
Large Scale ◽  
De Novo ◽  
Bloom Filter ◽  
Genomic Variation ◽  
De Bruijn Graph ◽  
Single Individual ◽  
Probabilistic Data Structure

AbstractThe assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps towards elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depends on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely.With ABySS 1.0, we originally showed that assembling the human genome using short 50 bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its re-design, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements.We present assembly benchmarks of human Genome in a Bottle 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual, yielding a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using less than 35 GB of RAM, a modest memory requirement by today’s standard that is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics’ Chromium data to further improve the scaffold contiguity of this assembly to 42 (15) Mbp.

Sign in / Sign up

Export Citation Format

Share Document