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Genome size

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Genome of extreme halophyte Puccinellia tenuiflora

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Taxonomy characteristics of Puccinellia tenuiflora are available at Flora of China (http://www.efloras.org/. tenuiflora ac- cording to Kato et al. tenuiflora genome size.. Our K-mer analysis showed that the genome size of extreme halophyte P. tenuiflora was 1.303 Gb (2n = 14) and the genome was complex, with 1.56% heterozygosity and 65.5% repeat content (Table 1).. tenuiflora genome size by the following formula: total K-mer number/K-mer depth.

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

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Meanwhile, at the lower end of the spectrum, the yellow drum (Sciaenidae: Nibea albiflora) has an estimated genome of 573–581 Mb and an assembly genome size of 596 Mb [11], and the Chin- ese sillago (Sillaginidae: Sillago sinica) has an estimated genome size of ~ 524 Mb, and an assembly genome size of just 534 Mb [33].

Intron and gene size expansion during nervous system evolution

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While these examples highlight several parameters potentially affecting the dy- namics of gene and genome size evolution at the organ- ismal level, our study indicates that biological parameters at the tissue and cellular level may also shape aspects of gene and genome architecture..

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

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The chloroplast genome of Atractylodes. The chloroplast genome size ranges from 152,294 bp ( A. All species have 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, in the chloroplast genome. The chloroplast genome is conserved similar to the majority of plants.

Genome sequence of the model rice variety KitaakeX

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Analysis of SNPs and InDels: We used MUMmer (ver- sion to align the Nipponbare and Zhenshan97 genomes to the KitaakeX genome using parameters -maxmatch -c 90 -l 40. Distribution of SNPs and InDels along the KitaakeX genome was visualized using Circos [38].. Further dividing the total bases by the coverage, provided an estimate of the genome size.

Novel genomic resources for shelled pteropods: A draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

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Fur- ther, when considering marine gastropod genome size estimates in the Animal Genome Size Database [50], genome sizes range from 430 Mbp to 5.88 Gbp with an average size of 1.86 Gbp. Roughly 350 million paired-end (PE) reads were used for the de novo assembly, but 50% of the assembly is still largely unresolved with fragments smaller than 893 bp.

Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

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The different destina- tions of transferred protein-coding genes and tRNA genes suggested that tRNA genes are much more con- served in the mt genome than the protein-coding genes, indicating their indispensable roles in mitochondria.. The comparison of mt genome size and GC content between S.

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations

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Metrics based on whole genome alignment to reference genome assembly. genome assembly plots, estimated genome size, datasets and species name for BUSCO analysis and email address to which the plots will be sent.. The gene space completeness analysis of the genome assembly is performed using the BUSCO pack- age version 3.0.2 [8] with genome mode.

Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues

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Results: The genome was sequenced using Illumina HiSeq 2000 and after assembly resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 31,769 (>. 2000 bp) predicted protein-coding genes across 27 tissue samples.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

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In the parallel implementation of all pipeline steps, we use genome size (in base pairs) as an additional fac- tor in the optimization of computational resources. Input data Single-cell, WGBS, WGBS, Single-cell WGBS RRBS, WGBS, WGBS. example, in the analysis of A. thaliana samples (genome size ∼135 mega base pairs), our parallel implementation of Trimmomatic (a java tool) sets the optimal number of jobs to 12 on a system with 88 cores and 386 GB RAM.. of threads fixed to 8 in the pipeline).

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

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In addition, the genome of the pearl oyster (Pinctada fucata) has a reported genome size of 990 Mb [82], but is not a species of true oyster, instead belonging to the family Pteriidae.. hindering scientifically-informed aquaculture science, and wider scientific understanding of the species. Moreover, both the sustainability of the Hong Kong oyster, and its.

The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity

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The generated clean reads from the 400 bp, 800 bp and 3- kb insert size libraries were used for the estimation of the genome size via JELLYFISH v1.116 [79] with a k-mer length of 17. The three annotation results were combined as the annotation of the predicted genes. The bench- marking sets of universal single-copy orthologues (BUS- COs) [21] were used to assess the completeness of the predicted genes with 1066 Arthropoda datasets.

Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus

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In addition, 546,642 and 618,772 clean reads were generated for Zhongshuang 4 and Nsa CMS by Miseq sequencing. genomes of Nsa CMS and maintainer lines were individu- ally assembled into a single, circular mapping molecule with a size of 153,449 bp (Genbank no. 1 Map of Nsa CMS chloroplast genome. Feature Nsa CMS Zhongshuang 4 Sinapis arvensis Genome size (bp .

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

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As a member of the tunicates, a sister taxonomic group to vertebrates, O.. dioica’ s genome size is 65 – 70 Mbp [8, 9], making it one of the smallest among all sequenced animals. Here, we present a chromosome-length assembly of the Okinawan O. Based on k-mer counting of the Illumina reads, the genome was estimated to contain ~ 50 Mbp (Fig. We corrected sequencing errors and local misas- semblies of the draft contigs with Nanopore reads using.

Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

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Our final assembly consists of 54 scaffolds, a N50 length of 2,038,020 bp, the longest length scaffold of 4,025,647 bp, the shortest length scaf- fold of 513 bp, a GC content of 47.59% and a size of 20.9 Mb (85.52% of the estimated genome size). We identified 5963 genes in the genome with an average length of 1620 bp and a mean GC-content of 47.26%. that occupied 55.07% of the genome.

Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice

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It seems that the physic nut MADS-box family has a smaller number of members (genome size 320 Mb) compared to those in rice (gen- ome size 466 Mb) and Arabidopsis (genome size 125 Mb) [25].

Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): Conserved genome structure, and ongoing low frequency recombination

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Intergenic spacers compose the bulk of the mt genome of land plants, accounting, for example, for about 80% in vascular plant mt genome size [16]. 2 Intron content of liverwort mitochondrial genomes. The species are ordered as in the phylogeny in Fig. In liverworts, the intergenic spacers constitute the largest portion of mt genomes (average. On average the complex thalloid mt genomes hold the largest spacer component.

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

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The similarities and differences of the cp genome be- tween C. avellana cv Tombul and other species,. including representatives of the Malpighiales, Fabales and Brassicales, were determined by a global alignment program, mVISTA [48]. avellana cv Tombul as a reference (Fig. Tombul had a similar cp genome size to the other species, which range from 152,217 bp to 161,303 bp (Tombul cp gen- ome size is 161,667 bp).

Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters

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The total size of the BGCs in B. subtilis MG27 is approxi- mately 176 kb and accounts for 4.2% of the genome size (Fig. This result is similar to the estimation of Bacillus velezensis FZB42, which is 8.5% [40]. Most of the BGCs from this group remain un- known, especially bacteriocins and terpenes (Fig. are anti- microbials reported in the past two decades. The total size of the BGCs is ap- proximately 500 kb, which accounts for 9.7% of the gen- ome (Fig.

Genome sequencing, annotation and exploration of the SO2-tolerant nonconventional yeast Saccharomycodes ludwigii

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Sequencing with Pac- Bio generated 585,118 reads (with a 445.3 coverage) which were de novo assembled into 20 contigs (with sizes ranging from 8.5 kbp to 2.7 Mbp, see supple- mentary Table S2) and an assembled genome of bp, corresponding to approximately 95% of the estimated genome size for UTAD17. In the end of the run 7 clearly separated bands, presumed to correspond to the 7 chromosomes of S.