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opennotspecifiedAug 2012View details →

FIGURE 9 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12

FIGURE 9. Holotype (MZUSP 147033) of Gastrotheca recava sp. nov.: Dorsal (A), Lateral (B) views of the head; Foot (C) and hand (D). Scale bar = 5 mm.

opennotspecifiedAug 2012View details →

FIGURE 8 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12

FIGURE 8. Holotype of Gastrotheca recava sp. nov. (MZUSP 147033): Dorsal (left) and ventral (right) views.

opennotspecifiedAug 2012View details →

FIGURE 4 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12

FIGURE 4. Advertisement call of Gastrotheca prasina sp. nov.: (A) Oscillogram containing four calls and; (B) An oscillogram of a section comprising a single call; (C) Spectrogram of the same call; (D) Amplitude spectrum of the same call. Calls were recorded about 20:00 h on 6th December 2009, air temperature was about 21ºC.

openNov 2022View details →

Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits

The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis,  and assembly validation for yellow starthistle (Centaurea solstitialis).

opencc-by-4.0Jun 2022View details →

Gaps and complex structurally variant loci in phased genome assemblies

Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.

Figure 5 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 5. Bayesian tree of Nematocera based on PCGRNA with heterogeneous models CAT+GTR in PhyloBayes. Numbers above the branches are posterior probabilities.

Figure 4. A in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 4. A LIGROOVE analysis for four datasets. The mean similarity score between sequences is represented by a coloured square, based on ALIGROOVE scores ranging from minus one, indicating a large difference in sequence composition from the remainder of the dataset (red coloration), to plus one, indicating similarity to all other comparisons (blue coloration).

Figure 3 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 3. Structures of AT-rich regions in three nematoceran species. The location and copy number of tandem repeat units are displayed by blue ovals. The non-repeat regions are indicated by red boxes. A, structure of AT-rich region in Plecia sp. B, structure of AT-rich region in Protaxymyia sp. C, structure of AT-rich region in Bradysia sp.

Figure 2 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 2. Relative synonymous codon usage (RSCU) and number of amino acids in protein-coding genes (PCGs) of the mitogenomes of eight nematoceran species. Leu1 = Leu (CUN); Leu2 = Leu (UUR); Ser1 = Ser (AGN); Ser2 = Ser (UCN).

Figure 1 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 1. Mitochondrial genomes of eight nematoceran species sequenced in this study. The circular maps were drawn with GENEIOUS v.10.2.2 (http://www.geneious.com/). The transcriptional direction is indicated by arrows.

Figure 6 in New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications

Figure 6. Bayesian tree of Nematocera based on PCGRNA with heterogeneous models CAT+GTR in PhyloBayes. Circles indicate that posterior probabilities = 100%. Squares indicate that posterior probabilities = 50–94%. Other posterior probabilities (95–99%) are given above the branches. Multiple sampling of different species from a single family, in addition to outgroups and Brachycera, are collapsed into triangles.

opencc-zeroJan 2023View details →

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Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.

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Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r2 between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

opencc-zeroMar 2023View details →

Fig. 7 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 7. Expression profiles analysis of OsFBNs under different temperature stresses. Eleven OsFBN genes in rice were detected for their transcript levels in leave tissues of seedlings at the three-leaf stage with different time intervals after the 35 ̊C (heat stress) and 6 ̊C (cold stress) stresses in the growth chamber, separately. The OsUBQ gene was used as a normalization control; data was measured as the mean values ± SD of three replicates, respectively.

Fig. 4 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 4. Phylogenetic and exon-intron structure analysis of FBN family genes in rice and Arabidopsis. The phylogenetic analysis was performed using the amino acid sequences of 25 FBN family proteins in rice and Arabidopsis (Left). The unrooted phylogenetic tree was generated by the neighbor-joining method and displayed using MEGA7 software. Numbers above or below branches of the evolution tree indicated the bootstrap values; The exon-intron structures of 25 FBN family genes in rice and Arabidopsis were analyzed (Right), the exons were represented by yellow boxes, the UTR by blue, black lines connecting two exons were introns. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 6. The in vitro lipid binding assays of PAP-domains. A and C, schematic representations of the mutant residues in OsFBN2 and OsFBN4 proteins in the in vitro lipid binding assays. B and D, the in vitro lipid-binding activity assays were performed by a fluorescence lipid probe P-96 (1 mM), fatty acids with C12:0, C14:0, C16:0, C18:0, C20:0, C22:0, with each (0.5 mM) of wild type (Wt) and mutant fusion protein (Mut) of PAP domains in OsFBN2 and OsFBN4 proteins, respectively. Detection experiments were performed with three biological replicates. * and ** symbols indicated the significant difference levels of P <0.05 or P <0.01 between mutant and wild type, respectively.

Fig. 5 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 5. Subcellular localization of CTP domains-fused GFP proteins. These constructs of p35S-FBN1-11-CTP-GFP or p35S-Trxm5-GFP, separately, were transiently expressed in Nicotiana benthamiana mesophyll cells. The co-localizations of fluorescence patterns of CTP domains of ten OsFBN proteins except OsFBN8 fused GFP were observed with the autofluorescence of chlorophyll in chloroplasts in protoplasts. The Trxm5-GFP was used as a chloroplast marker.

Fig. 3 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 3. PKC domain analysis of FBN11 clade in plants. A, Homology analysis of PKC domain sequences in FBN11 clades; B, evolutionary tree analysis of PKC domain in five plant species (Oryza sativa (Os), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At), Glycine max (Gm), and Zea mays (Zm)) and algae (Monoraphidium neglectum (Mon), Chlorella sorokiniana (Chlo), Chlamydomonas sp. UWO 241 (Chla), and Haemato coccus lacustris (Hae); C, the conserved motif analysis of PKC domain in FBN11 protein clades in higher plants.

Fig. 2 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 2. Box-plot graphs and motif analysis of CTP and PAP-domain in plants. The protein sequences of CTP domains and PAP domains were analyzed in six plant species: Selaginella moellendorffii (Smo), Physcomitrella patens (Ppa), Arabidopsis thaliana (At), Glycine max (Gm), Oryza sativa (Os), and Zea mays (Zm), The grand average of hydropathicity (GRAVY) and isoelectric point (pI) of CTP domains of FBN1-11 protein clades were showed in A and B, respectively; The GRAVY and pI of PAP domains in FBN1-11 protein clades were showed in C and D, respectively; The dotted line represented the average values of GRAVY and pI, respectively; The conserved motif sequence of PAP domains in these plants were showed in E.

Fig. 1 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 1. Phylogenetic tree analysis of 121 fibrillin family proteins from 10 representative species. The neighbor-joining tree was constructed using the sequences of 121 fibrillin family proteins in ten representative species: Synechococcus sp. PCC 7002 (Ssp), Erysimum siliculosus (Esi), Emiliania huxleyii (Ehu), Thalassiosira pseudonana (Tps), Chlamydomonas reinhardtii (Cre), Volvox carteri (Vca), Physcomitrella patens (Ppa), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At) and Oryza sativa (Os). Bootstrap values were indicated on the branches. Each fibrillin protein was labeled by its name (Table S3). The green and red color meant the proteins present in algae or terrestrial plant, respectively; the blue color represents the proteins present in both algae and terrestrial plants. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)