scholarly journals A target enrichment bait set for studying relationships among ostariophysan fishes

2018 ◽  
Author(s):  
Brant C. Faircloth ◽  
Fernando Alda ◽  
Kendra Hoekzema ◽  
Michael D. Burns ◽  
Claudio Oliveira ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Sequence Data ◽  
Evolutionary Relationships ◽  
List Type ◽  
Target Enrichment ◽  
Large Numbers ◽  
Ostariophysan Fishes ◽  
Nuclear Loci ◽  
Enrichment Experiments ◽  
Low Coverage

SummaryTarget enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder.In this manuscript, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages.We perform a series of enrichment experiments using this bait set across the ostariophysan Tree of Life, from the deepest splits among the major groups (>150 MYA) to more recent divergence events that have occured during the last 50 million years.Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

scholarly journals Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

2018 ◽  
Vol 20 (4) ◽  
pp. 1542-1559 ◽  
Author(s):  
Damla Senol Cali ◽  
Jeremie S Kim ◽  
Saugata Ghose ◽  
Can Alkan ◽  
Onur Mutlu
Keyword(s):  
Sequence Analysis ◽  
Genome Assembly ◽  
Sequence Data ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Memory Usage ◽  
Sequencing Technology ◽  
Assembly Pipeline ◽  
And Performance ◽  
Polishing Tool

Abstract Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Cross-reactive, natural IgG recognizing L. major promote parasite internalization by dendritic cells and promote protective immunity

2021 ◽  
Author(s):  
Filiz Dermicik ◽  
Susanna Lopez Kostka ◽  
Stefan Tenzer ◽  
Ari Waisman ◽  
Esther Von Stebut
Keyword(s):  
Dendritic Cells ◽  
B Cell ◽  
Protective Immunity ◽  
Normal Mouse ◽  
Leishmania Major ◽  
Mouse Serum ◽  
List Type ◽  
Susceptibility To Infection ◽  
Large Numbers

Abstract In cutaneous leishmaniasis, infection of dendritic cells (DC) is essential for generation of T cell-dependent protective immunity. DC acquires Leishmania major through Fc receptor (FcR)-mediated uptake of complexes comprising antibodies bound to parasites. We now assessed the development of the initial B cell and DC response to the parasite itself and if natural IgG play a role. L. major parasites display large numbers of phospholipids on their surface. Parasites were opsonized with normal mouse serum (NMS), or serum containing anti-phospholipid IgG (PL). We found that L. major bound to PL which significantly enhanced parasite phagocytosis by DC as compared to NMS. Similar results were obtained with cross-reactive human PL antibodies using myeloid primary human DC. In addition, mice infected with PL-opsonized parasites showed significantly improved disease outcome compared to mice infected with NMS-opsonized parasites. Finally, IgMi mice, which produce membrane-bound IgM only and no secreted antibodies, displayed increased susceptibility to infection as compared to wild types. Interestingly, once NMS was administered to IgMi mice, their phenotype was normalized to that of wild types. Upon incubation with IgG-opsonized parasite (IgG derived from infected mice or using PL antibodies), also the IgMi mice were able to show superior immunity. Our findings suggest that “natural” cross-reactive antibodies (e.g., anti-PL Ab) in NMS bind to pathogens to facilitate phagocytosis, which leads to induction of protective immunity via preferential DC infection. Prior L. major-specific B cell-priming does not seem to be absolutely required to facilitate clearance of this important human pathogen in vivo. Key messages We found that anti-phospholipid (anti-PL) antibodies enhance phagocytosis of L. major by DCs. We also found that normal mouse sera have natural antibodies that can imitate PL specific antibodies. Using different genetically modified mice, we found that these antibodies can be IgG, not only IgM.

scholarly journals Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

2021 ◽  
Author(s):  
Jiayi Ji ◽  
Donavan J. Jackson ◽  
Adam D. Leaché ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Likelihood Method ◽  
Recent Analysis ◽  
The Past ◽  
Rapid Speciation ◽  
Full Likelihood ◽  
Nuclear Loci ◽  
Robust Evidence

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow.

scholarly journals An accurate assignment test for extremely low‐coverage whole‐genome sequence data

2021 ◽  
Author(s):  
Giada Ferrari ◽  
Lane M. Atmore ◽  
Sissel Jentoft ◽  
Kjetill S. Jakobsen ◽  
Daniel Makowiecki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Assignment Test ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Low Coverage

scholarly journals De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akifumi Azuma ◽  
Fumiya Taniguchi ◽  
Toshiya Yamamoto ◽  
Akihiko Sato ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genome Structure ◽  
Table Grape ◽  
Sequencing Analysis ◽  
Entire Genome ◽  
Table Grapes ◽  
Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

Amanita mansehraensis, a new species in section Vaginatae from Pakistan

Phytotaxa ◽  
2019 ◽  
Vol 409 (4) ◽  
pp. 189-201 ◽  
Author(s):  
MALKA SABA ◽  
DANNY HAELEWATERS ◽  
MUHAMMAD FIAZ ◽  
ABDUL NASIR KHALID ◽  
DONALD H. PFISTER
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Large Subunit ◽  
Pine Forests ◽  
Evolutionary Relationships ◽  
Internal Transcribed Spacer Region ◽  
Bayesian Inferences ◽  
A New Species

A new species of Amanita subgenus Amanita sect. Vaginatae is described and illustrated based on material collected in pine forests in district Mansehra, Khyber Pakhtoonkhaw, Pakistan. Amanita mansehraensis is recognized by the presence of a light brown or light greyish olive pileus with strong brown or deep brown pileus center; non-appendiculate, rimose, sulcate or plicate striate pileus margin; subglobose to ellipsoid basidiospores; and a saccate volva. The internal transcribed spacer region (ITS) and large subunit of the nuclear ribosomal RNA gene (nrLSU) were used for the delimitation of this species based on sequence data. The evolutionary relationships of A. mansehraensis with other species of Amanita were inferred by means of Maximum Likelihood and Bayesian inferences of the nrLSU dataset and concatenated ITS+nrLSU dataset. Amanita mansehraensis is most closely related to A. brunneofuliginea, A. pseudovaginata, and the recently described A. glarea.

scholarly journals The gene-rich genome of the scallop Pecten maximus

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Nathan J Kenny ◽  
Shane A McCarthy ◽  
Olga Dudchenko ◽  
Katherine James ◽  
Emma Betteridge ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Atlantic Coast ◽  
Shallow Waters ◽  
Pharmaceutical Companies ◽  
Marine Bivalve ◽  
Pecten Maximus ◽  
Assembly Sequence ◽  
Algal Toxins ◽  
Large Numbers

Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. Findings Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. Conclusions The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

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