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17 results for “Onychostoma”
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
FIGURE 3 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 3. Front view of head of Onychostoma krongnoensis (a) female holotype UNS00805, 205 mm SL, (b) immature paratype UNS00821, 123 mm SL, (c) male paratype UNS00825, 214 mm SL; O. dongnaiensis (e) female holotype UNS00851, 172 mm SL, (f) female paratype UNS00852, 196 mm SL, (g) male paratype ZRC 54625, 157 mm SL; O. leptura (i) female UNS00684, 186 mm SL. Ventral view of head of O. krongnoensis, wide mouth (d) male paratype UNS00825; O. dongnaiensis, wide mouth (h) female holotype UNS00851; O. leptura, wide mouth (j) female UNS00684; O. meridionale, moderate mouth (k) immature UNS00826, 108 mm SL; O. uniforme, narrow mouth (l) female UNS00689, 130 mm SL. Scale 10 mm.
FIGURE 2 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 2. Lateral view of Onychostoma krongnoensis specimens (a) female holotype UNS00805 in life, (b) female holotype UNS00805 in preservative, (c) male paratype UNS00825 in preservative. Scale 10 mm.
FIGURE 1 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 1. Type localities of Onychostoma krongnoensis (black star) and O. dongnaiensis (white star).
FIGURE 6 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 6. Maximum-likelihood tree based on 16S ribosomal RNA mitochondrial gene sequences for species of Onychostoma (Wang et al. 2012) and for the outgroup Percocypris pingi. Numbers on branches are ML bootstrap values (values ≥ 45% shown).
FIGURE 5 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 5. Lateral view of Onychostoma dongnaiensis specimens (a) female holotype UNS00851 in life, (b) female holotype UNS00851 in preservative, (c) male paratype ZRC 54625 in preservative. Scale 10 mm.
FIGURE 4 in Two new species of shovel-jaw carp Onychostoma (Teleostei: Cyprinidae) from southern Vietnam
FIGURE 4. High elevation main river at type locality of Onychostoma krongnoensis. Habitats altering from fast flowing pool (a) with bed of detritus and falling leaves, running to riffles (c) and swift current (b) over bedrock, large boulder and cobble substrates covered with periphyton (sites continuous); low elevation main river at type locality of Onychostoma dongnaiensis (d) running to riffles.
FIGURE 3 in Onychostoma brevibarba, a new cyprinine fish (Pisces: Teleostei) from the middle Chang Jiang basin in Hunan Province, South China
FIGURE 3 (a) Type locality of O. brevibarba: hill stream with clear water and mixed substrate including sand, gravel and boulders; (b) reservoir into which the hill stream flows.
FIGURE 5 in Onychostoma brevibarba, a new cyprinine fish (Pisces: Teleostei) from the middle Chang Jiang basin in Hunan Province, South China
FIGURE 5 Bayesian (BI) tree inferred from combined genes. Numbers at major internal nodes are Bayesian posterior probability values and bootstrap values for BI/ML tree.
FIGURE 2 in Onychostoma brevibarba, a new cyprinine fish (Pisces: Teleostei) from the middle Chang Jiang basin in Hunan Province, South China
FIGURE 2 Ventral view of the oromandibular structures. (a) O. brevibarba, IHB 2011062588, 86.0 mm SL; (b) O. minnanense, IHB 74V0408, 77.9 mm SL; (c) O. barbatulum, IHB 20070601405, 83.1 mm SL. Abbreviations: rf, rostral fold; rb, rostral barbels; ul, upper lip; pg, postlabial groove; lj, lower jaw; mb, maxillary barbels; ll, lower lip. Scale bars = 5 mm.
FIGURE 1 in Onychostoma brevibarba, a new cyprinine fish (Pisces: Teleostei) from the middle Chang Jiang basin in Hunan Province, South China
FIGURE 1 (a) Onychostoma brevibarba sp. nov., holotype, IHB 2011062587, 86.0 mm SL, Mi Shui in Hengdong County, Hunan Province, China; (b) young individual, IHB 2011051732, 72.8 mm SL; (c) freshly captured specimen; (d) live individual in a stream flowing into a reservoir; photo by E Zhang, May 2011. Scale bars = 1 cm.
FIGURE 4 in Onychostoma brevibarba, a new cyprinine fish (Pisces: Teleostei) from the middle Chang Jiang basin in Hunan Province, South China
FIGURE 4 Distribution of Onychostoma brevibarba. Black circles indicate sites at which O. brevibarba was captured.
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
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Figure 2 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 2 Comparison of codon usage in mitochondrial genomes of Onychostoma lepturuma Relative synonymous codon usage (RSCU) in the Onychostoma lepturum mitogenome. Codon families are provided on the X-axis, and the RSCU values, on the Y-axis b Codon distribution in the Onychostoma lepturum mitogenome. CDspT, codons per thousand codons. Codon families are provided on the X-axis.
Figure 1 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 1 Gene map of the mitochondrial genome of Onychostoma lepturum. Two rRNA genes (in red); 13 coding genes (in green); 22 tRNA genes and control region (D-loop) (in yellow). (Color figure online).
Supplementary material 1 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Table S1
Figure 3 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 3 Phylogenetic trees derived from Maximum-Likelihood (ML) and Neighbor Joining (NJ) approaches based on whole mitochondrial genomes. The numbers on the nodes are the bootstrap values of ML/NJ. The number after the species name is the GenBank Accession Number.
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