Find research datasets worth reusing

FIGURE 6 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 6. Phylogenetic tree of four sequenced assassin bugs. Bayesian inference and Maximum likelihood analysis inferred from all genes recovered the same topological structure. Bootstrap values and Bayesian posterior probabilities are indicated at each node.

FIGURE 3 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 3. Predicted secondary structure of the rrnL in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 2 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 2. Inferred secondary structures of 22 tRNAs of S. flavipes. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 4 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 4. Predicted secondary structure of the rrnS in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 5 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 5. (A) The conserved region of the mitochondrial control region of S. flavipes, A. dohrni, T. dimidiata and V. hoffmanni. (B) The structural organization of the mitochondrial control region of S. flavipes. The control region flanking genes rrnS, trnI (I), trnQ (Q), and trnM (M) are represented in purple and green boxes. The light blue boxes with roman numerals indicate the tandem repeat region. "G+C" indicates high G+C content region. "A+T" indicates high A+T content region. The black box indicates G element.

FIGURE 1 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 1. Map of the mtochondrial genome of S. flavipes. Direction of gene transcription is indicated by the arrows. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows and large non-coding regions (>100 bp) as cyan rectangles. tRNA genes are labeled according to single-letter IUPAC-IUB abbreviations (L1: UUR; L2:CUN; S1:AGN; S2:UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC Skew is plotted as the deviation from the average GC skew of the entire sequence. Ticks in the inner cycle indicate the sequence length.

opennotspecifiedSep 2000View details →

FIG. 1 in OPINION Testing for the accumulation of deleterious mutations in asexual eukaryote genomes using molecular sequences

FIG. 1. Phylogeny of representative sexual and asexual Lachnidae with estimates of the numbers of replacement and silent substitutions for EF1a and CO2 on each branch. See text for description of estimation of the numbers of substitutions in each category. Phylogeny is from Normark (2000).

opencc-zeroSep 2021View details →

Rhizophora complete chloroplast genome sequences

Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of Rhizophora species. Throughout the Indian Ocean, R. stylosa and R. mucronata appear as a young phylogenetic group with expansion of R. mucronata towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 R. mucronata provenances across a >4,200 km coastal stretch in the WIO using R. stylosa as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the R. stylosa chloroplast genome. A total of 58 mutations in R. mucronata encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other R. mucronata haplogroups as it was from R. stylosa. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO Rhizophora mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of R. mucronata lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.

opencc-zeroSep 2021View details →

Genome sequencing of Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), a potential biological control agent for Mikania micrantha

The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is a potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most invasive weeds worldwide). To date, only a few studies have investigated plant bugs. Here, we performed a chromosome-level genome assembly of P. micranthus using MGISEQ-2000 short-read, Nanopore, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) techniques. The assembled genome was 712.72 Mb in size, with a contig N50 of 16.84 Mb. Using the Hi-C technique, 71 scaffolds were assembled into 15 chromosomes, accounting for 99.96%. We predicted 11,746 protein-coding genes in P. micranthus with 96.20% complete benchmarking universal single-copy orthologs. Phylogenomic analysis showed that P. micranthus and two other Miridae bugs (Apolygus lucorum and Nesidiocoris tenuis) diverged from the common ancestor approximately 200.01 million years ago. Chromosome synteny analysis between P. micranthus and A. lucorum indicated high-level synteny. Many gene families including chemosensory genes and digestive and detoxification enzyme genes—were significantly expanded in the P. micranthus genome. These expanded gene families may indicate the bug to adapt to the single host plant. This high-quality chromosome-level genome assembly provides an invaluable resource for further molecular and evolutionary research on mirid bugs and also provides a basis for further research on biological control mechanisms for M. micrantha.

opencc-by-4.0Oct 2021View details →

Automated application to assist in detecting novel gene-disease associations following whole genome sequencing

Results files, analysis scripts and original software from TierUp reanalysis performed on June 2020. These data contribute to the publication titled "Automated reanalysis application to assist in detecting novel gene-disease associations following whole genome sequencing".  <ul> <li> tierup_v0-3-0.tar.gz - source code used in the reanalysis </li> <li> tierup_results_summary.tar.gz - raw data and python code for publication figures </li> </ul>

opencc-by-4.0Dec 2021View details →

Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat

Oxford Nanopore assembly of Triticum turgidum ssp. dicoccoides, cv. G305-3M.

opencc-zeroDec 2022View details →

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence

Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

opencc-by-4.0Jan 2023View details →

Dataset: Complete Genome Sequences of Sathuperi and Shamonda viruses isolated in Japan

This file contains supplementary information corresponding to the manuscript: "Complete Genome Sequences of Sathuperi and Shamonda viruses isolated in Japan".

opencc-zeroJan 2023View details →

Supplemental data for: Classification of the Celastrales based on integration of genomic, morphological, and Sanger-sequence characters

We present the best sampled phylogenetic analysis of Celastrales, with respect to both character and taxon sampling, and use it to present a natural classification of the order. Parnassiaceae are highly supported as sister to Celastraceae; we recognize both families as distinct. Pottingeria is highly supported as a member of an early derived lineage within Celastraceae. We recognize and circumscribe 13 subfamilies in Celastraceae, including the new subfamilies Crossopetaloideae, Maytenoideae, Microtropioideae, Monimopetaloideae, and Salaciopsioideae. We identified five genera that likely require generic recircumscriptions: Cassine, Elachyptera, Gymnosporia, Salacia, and Semialarium. Genera that had not been previously sampled in Sanger-sequence-based studies are resolved as follows: Arnicratea is sister to Reissantia, Bequaertia is in a clade with Campylostemon and Tristemonanthus, Goniodiscus is sister to Wilczekra, Ptelidium is nested within Elaeodendron, and Tetrasiphon is most closely related to Gyminda.

FIGURE 7 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 7. Phylogenetic network of individuals examined in this study produced by the neighbor net algorithm. Tips are labeled by individual codes described in Table 1. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento River Redband Trout (O. m. stonei) are show in bold. The outgroup species, Lahontan Cutthroat Trout (O. clarkii henshawi) is indicated.

FIGURE 3 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 3. Admixture plots from the population genetics data set. Number of genetic clusters (K) presented for K = 2–6 from all samples (n = 318) analyzed in a population genetics framework. Admixture analysis was conducted in NGSAdmix with an optimal K = 3. Labeling of x-axis is according to Group as in Table 1: CAGT, California Golden Trout; KRRT, Kern River Rainbow Trout; LKGT, Little Kern Golden Trout; CRT, Coastal Rainbow Trout; EGLK, Eagle Lake Rainbow Trout; HRNB, Hatchery Rainbow Trout; MRRB, McCloud River Redband Trout; REDB, all other Redband Trout.

FIGURE 6 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 6. Species tree produced by SVDQuartets. The species tree branch lengths are equal and bootstrap support was maximal for all nodes and not shown. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated with McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) in bold text. For Rainbow Trout subspecies, sampling locations are labeled with a four-letter code corresponding to Figure 1 and Table 1. The two samples of Lahontan Cutthroat Trout (O. clarkii henshawi) are labeled as LCT.

FIGURE 2 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 2. Principal Component Analyses. The first two Principal Components (PCs) are presented for all samples (n = 318) in the population genetics analysis in A and Redband Trout samples (n = 204) in B. Genotype likelihoods were generated separately for the PCs presented in each panel. In A points are color coded by Group corresponding broadly to lineage, and further condensed into a Major Group by consolidating the California Golden Trout Complex and represented by shape (Table 1). In B, points are colored by watershed and the same shape applied to the Major Group (MRRB and REDB). Abbreviations for Major Group are explained in the text.

FIGURE 1 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 1. Map of key features and distributions of key lineages in this study. The distribution of Coastal Rainbow Trout (Oncorhynchus mykiss irideus) is shown in grey shading. Other lineages are labeled in different colors. Distributions were retrieved from the PISCES database (pisces.ucdavis.edu, "Historic Range—Expert Opinion") except for Warner Lakes Redband Trout (O. m. ssp.), which is represented by a polygon of hydrologic unit code (HUC) 17120007. Sampling locations used in phylogenetic analyses are indicated with a four-letter code that corresponds to Table 1 and Supplemental Table S1. Samples of O. m. gairdnerii from Idaho are not shown.

FIGURE 5 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 5. Maximum Likelihood (ML) tree (A) and ML consensus tree (B). In both panels subspecies of Rainbow Trout (Oncorhynchus mykiss) are indicated along with members of the Golden Trout Complex. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) are indicated with bold text. Individual sample names are provided at tips and further described in Table 1. In 5A, nodes receiving Shimodaira-Hasegawa approximate Likelihood Ratio Test scores> 80 and bootstrap support (BS)> 95% are indicated with a diamond. In 5B, two spans of bootstrap support are presented, with 100%> BS> 95% as solid black circles and 95%> BS> 90% as grey circles at nodes.