GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data

Whole-genome sequence analysis of the evolutionary history of the reef-building coral genus Acropora (Scleractinia, Cnidaria)

A major goal of evolutionary biology is to understand the roles of evolutionary and ecological factors in rapid speciation and diversification. Introgression and ancient large-scale/whole genome duplication (paleopolyploidy) have been hypothesized to promote on rapid speciation leading to diversification. In addition, diversification can be promoted by ‘ecological opportunity’ created by extinction of competitors or the colonization of a new area. Reef-building corals are the foundation of diverse tropical ecosystems, but are currently under threat due to the sensitivity of corals to climate change and anthropogenic factors. Acropora (Anthozoa: Acroporidae) is one of the most diverse genera of reef-building corals, including more than 150 species, and based on the fossil record has dominated IndoPacific reefs in past 3 Million Years, yet the evolutionary and ecological factors associated with its diversification and the rise to dominance are unclear. Understanding the evolutionary history of this group during its rise to dominance may help understanding their current and future responses to global change. In this dissertation, I used genomic data of Acropora generated by Dr. Chuya Shinzato to investigate its evolutionary history and illuminate the roles of introgression, largescale genome duplication, and ecological opportunity in its diversification and the rise to dominance. In the first chapter, I reviewed recent studies of Acropora. In the second chapter, I examined the roles of introgression in Acropora. I found that a major introgression event and widespread gene flow occurred in five Acropora species, and that introgression genes evolved faster than others. In the third chapter, I examined the roles of climate change in the rise to dominance of Acropora. I found that Acropora lineages had an experience of population expansion after a climatedriven mass extinction event in the Plio-Pleistocene, suggesting ecological opportunity facilitated the rise to dominance of Acropora. In the fourth chapter, I examined evidence for large-scale genome duplication and its consequences in Acropora. I found a large-scale genome duplication event likely occurred in Acropora and duplicated genes play important roles in the diversification of Acropora. Finally, in the fifth chapter, I discussed limitations and future directions arising from this dissertation. Collectively, this dissertation suggests that introgression, climate change, and large-scale genome duplication play important roles in the evolutionary history of Acropora.Okinawa Institute of Science and Technology Graduate Universit

The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals

Reef-building corals provide the structural basis for one of Earth\u27s most spectacular and diverse-but increasingly threatened-ecosystems. Modern Indo-Pacific reefs are dominated by species of the staghorn coral genus Acropora, but the evolutionary and ecological factors associated with their diversification and rise to dominance are unclear. Recent work on evolutionary radiations has demonstrated the importance of introgression and ecological opportunity in promoting diversification and ecological success. Here, we analyze the genomes of five staghorn coral species to examine the roles of introgression and ecological opportunity in the rise to dominance of Acropora. We found evidence for a history marked by a major introgression event as well as recurrent gene flow across species. In addition, we found that genes with topologies mismatching the species tree are evolving faster, which is suggestive of a role for introgression in spreading adaptive genetic variation. Demographic analysis showed that Acropora lineages profited from climate-driven mass extinctions in the Plio-Pleistocene, indicating that Acropora exploited ecological opportunity opened by a new climatic regime favoring species that could cope with rapid sea-level changes. Collectively, the genomes of reef-building corals have recorded an evolutionary history shaped by introgression and climate change, suggesting that Acropora-among most vulnerable corals to stressors-may be critical for understanding how reefs track the impending rapid sea-level changes of the Anthropocene

Characterization of the ompL1 gene of pathogenic Leptospira species in China and cross-immunogenicity of the OmpL1 protein

<p>Abstract</p> <p>Background</p> <p>The usefulness of available vaccine and serological tests for leptospirosis is limited by the low cross-reactivity of antigens from numerous serovars of pathogenic <it>Leptospira </it>spp. Identification of genus-specific protein antigens (GP-Ag) of <it>Leptospira </it>would be important for development of universal vaccines and serodiagnostic methods. OmpL1, a transmembrane porin of pathogenic leptospires, was identified as a possible GP-Ag, but its sequence diversity and immune cross-reactivity among different serovars of pathogenic leptospires remains largely unknown.</p> <p>Results</p> <p>PCR analysis demonstrated that the <it>ompL1 </it>gene existed in all 15 official Chinese standard strains as well as 163 clinical strains of pathogenic leptospires isolated in China. In the standard strains, the <it>ompL1 </it>gene could be divided into three groups (<it>ompL1/1</it>, <it>ompL1/2 </it>and <it>ompL1/3</it>) according to their sequence identities. Immune electron microscopy demonstrated that all products of the different gene types of <it>ompL1 </it>are located on the surface of leptospires. The microscopic agglutination test revealed extensive yet distinct cross-immunoagglutination among the antisera against recombinant OmpL1 (rOmpL1) and leptospiral strains belonging to different <it>ompL1 </it>gene types. These cross-immunoreactions were further verified by ELISAs using the OmpL1 proteins as the coated antigens in serum samples from 385 leptospirosis patients. All the antisera against rOmpL1 proteins could inhibit <it>L. interrogans </it>strain Lai from adhering to J774A.1 cells. Furthermore, immunization of guinea pigs with each of the rOmpL1 proteins could cause cross-immunoprotection against lethal challenge with leptospires from different <it>ompL1 </it>gene types.</p> <p>Conclusion</p> <p>Three types of the <it>ompL1 </it>gene are present in pathogenic leptospires in China. OmpL1 is an immunoprotective GP-Ag which should be considered in the design of new universal vaccines and serodiagnostic methods against leptospirosis.</p

TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python-TREEasy-that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree and RaxML-NG), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the "WGD clade" of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy)

Ampere-hour-scale soft-package potassium-ion hybrid capacitors enabling 6-minute fast-charging

Extreme fast charging of Ampere-hour (Ah)-scale electrochemical energy storage devices targeting charging times of less than 10 minutes are desired to increase widespread adoption. However, this metric is difficult to achieve in conventional Li-ion batteries due to their inherent reaction mechanism and safety hazards at high current densities. In this work, we report 1 Ah soft-package potassium-ion hybrid supercapacitors (PIHCs), which combine the merits of high-energy density of battery-type negative electrodes and high-power density of capacitor-type positive electrodes. The PIHC consists of a defect-rich, high specific surface area N-doped carbon nanotube-based positive electrode, MnO quantum dots inlaid spacing-expanded carbon nanotube-based negative electrode, carbonate-based non-aqueous electrolyte, and a binder- and current collector-free cell design. Through the optimization of the cell configuration, electrodes, and electrolyte, the full cells (1 Ah) exhibit a cell voltage up to 4.8 V, high full-cell level specific energy of 140 Wh kg-1 (based on the whole mass of device) with a full charge of 6 minutes. An 88% capacity retention after 200 cycles at 10 C (10 A) and a voltage retention of 99% at 25 ± 1 °C are also demonstrated

An evolutionary driver of interspersed segmental duplications in primates

Background The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein (NPIP). Results Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. Conclusions LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution

A high-quality bonobo genome refines the analysis of hominid evolution

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3,4,5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome