scholarly journals Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes

Marine Drugs ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. 466 ◽  
Author(s):  
Ronghua Li ◽  
Michaël Bekaert ◽  
Luning Wu ◽  
Changkao Mu ◽  
Weiwei Song ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Average Length ◽  
Bioactive Molecules ◽  
Asian Countries ◽  
Marine Gastropod ◽  
Sequencing Technologies ◽  
First Time ◽  
Aquaculture Development ◽  
Simple Sequence

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers

2020 ◽  
Author(s):  
Yuansheng Liu ◽  
Xiaocai Zhang ◽  
Quan Zou ◽  
Xiangxiang Zeng
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Complementary Strand ◽  
Short Reads ◽  
Sequencing Technologies ◽  
Computational Resources

Abstract Summary Removing duplicate and near-duplicate reads, generated by high-throughput sequencing technologies, is able to reduce computational resources in downstream applications. Here we develop minirmd, a de novo tool to remove duplicate reads via multiple rounds of clustering using different length of minimizer. Experiments demonstrate that minirmd removes more near-duplicate reads than existing clustering approaches and is faster than existing multi-core tools. To the best of our knowledge, minirmd is the first tool to remove near-duplicates on reverse-complementary strand. Availability and implementation https://github.com/yuansliu/minirmd. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Transcriptome Analysis of ‘Haegeum’ Gold Kiwifruit Following Ethylene Treatment to Improve Postharvest Ripening Quality

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 487 ◽  
Author(s):  
Shimeles Tilahun ◽  
Han Ryul Choi ◽  
Hyok Kwon ◽  
Sung Min Park ◽  
Do Su Park ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Average Length ◽  
Titratable Acidity ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Sequencing Platform ◽  
Ethylene Treatment ◽  
Control Fruit

Fruit ripening involves changes in physical, physiological and metabolic activities through the actions of enzymes and regulatory genes. This study was initiated to identify the genes related to the ripening of kiwifruit. Gold ‘Haegeum’ kiwifruit is a yellow-fleshed kiwifruit cultivar usually used for fresh marketing. The fruit is harvested at a physiologically mature but unripe stage for proper storage, marketing distribution and longer shelf life. To identify the differentially expressed genes (DEGs) during ripening, fruit treated with ethylene were compared with control fruit that ripened naturally without ethylene treatment. Firmness, respiration rate, ethylene production rate, total soluble solids (TSS), titratable acidity (TA), brix acid ratio (BAR) and overall acceptability were taken during the study as fruit ripening indicators. Total mRNAs were sequenced by Illumina high-throughput sequencing platform and the transcriptome gene set was constructed by de novo assembly. We identified 99,601 unigenes with an average length of 511.77 bp in transcriptome contigs. A total of 28,582 differentially expressed unigenes were identified in the ethylene treatment vs. control. Of these 28,582 unigenes, 13,361 and 15,221 genes were up- and downregulated, respectively, in the treated fruit. The results also showed that 1682 and 855 genes were up- and downregulated, respectively, more than 2-fold at p < 0.05 in fruit treated with ethylene as compared with the control fruit. Moreover, we identified 75 genes showing significantly different expression; 42 were upregulated, and 33 were downregulated. A possible category of the identified ripening-related genes was also made. The findings of this study will add to the available information on the effect of ethylene treatment on ripening and the related changes of kiwifruit at the genomic level, and it could assist the further study of genes related to ripening for kiwifruit breeding and improvement.

scholarly journals Factorbook Motif Pipeline: A de novo motif discovery and filtering web server for ChIP-seq peaks

2015 ◽  
Author(s):  
Bong-Hyun Kim ◽  
Jiali Zhuang ◽  
Jie Wang ◽  
Zhiping Weng
Keyword(s):  
Motif Discovery ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Statistical Tests ◽  
Web Server ◽  
Biological Processes ◽  
Web Based ◽  
Sequencing Technologies ◽  
De Novo Motif Discovery

Summary: High-throughput sequencing technologies such as ChIP-seq have deepened our understanding in many biological processes. De novo motif search is one of the key downstream computational analysis following the ChIP-seq experiments and several algorithms have been proposed for this purpose. However, most web-based systems do not perform independent filtering or enrichment analyses to ensure the quality of the discovered motifs. Here, we developed a web server Factorbook Motif Pipeline based on an algorithm used in analyzing ENCODE consortium ChIP-seq datasets. It performs comprehensive analysis on the set of peaks detected from a ChIP-seq experiments: (i) de novo motif discovery; (ii) independent composition and bias analyses and (iii) matching to the annotated motifs. The statistical tests employed in our pipeline provide a reliable measure of confidence as to how significant are the motifs reported in the discovery step. Availability: Factorbook Motif Pipeline source code is accessible through the following URL. https://github.com/joshuabhk/factorbook-motif-pipeline

scholarly journals Fast sequence-based microsatellite genotyping development workflow

2019 ◽  
Author(s):  
Olivier Lepais ◽  
Emilie Chancerel ◽  
Christophe Boury ◽  
Franck Salin ◽  
Aurélie Manicki ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
De Novo ◽  
Microsatellite Genotyping ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Genomic Resource ◽  
Analytical Frameworks ◽  
Different Levels

AbstractApplication of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

scholarly journals Index suffix–prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression

2018 ◽  
Vol 35 (12) ◽  
pp. 2066-2074 ◽  
Author(s):  
Yuansheng Liu ◽  
Zuguo Yu ◽  
Marcel E Dinger ◽  
Jinyan Li
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Reference Sequence ◽  
Supplementary Information ◽  
The Novel ◽  
Rna Seq ◽  
File Size ◽  
Sequencing Technologies ◽  
Efficient Storage ◽  
Merging Process

Abstract Motivation Advanced high-throughput sequencing technologies have produced massive amount of reads data, and algorithms have been specially designed to contract the size of these datasets for efficient storage and transmission. Reordering reads with regard to their positions in de novo assembled contigs or in explicit reference sequences has been proven to be one of the most effective reads compression approach. As there is usually no good prior knowledge about the reference sequence, current focus is on the novel construction of de novo assembled contigs. Results We introduce a new de novo compression algorithm named minicom. This algorithm uses large k-minimizers to index the reads and subgroup those that have the same minimizer. Within each subgroup, a contig is constructed. Then some pairs of the contigs derived from the subgroups are merged into longer contigs according to a (w, k)-minimizer-indexed suffix–prefix overlap similarity between two contigs. This merging process is repeated after the longer contigs are formed until no pair of contigs can be merged. We compare the performance of minicom with two reference-based methods and four de novo methods on 18 datasets (13 RNA-seq datasets and 5 whole genome sequencing datasets). In the compression of single-end reads, minicom obtained the smallest file size for 22 of 34 cases with significant improvement. In the compression of paired-end reads, minicom achieved 20–80% compression gain over the best state-of-the-art algorithm. Our method also achieved a 10% size reduction of compressed files in comparison with the best algorithm under the reads-order preserving mode. These excellent performances are mainly attributed to the exploit of the redundancy of the repetitive substrings in the long contigs. Availability and implementation https://github.com/yuansliu/minicom Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 287
Author(s):  
Kunyuan Guo ◽  
Jie Chen ◽  
Yan Niu ◽  
Xianming Lin
Keyword(s):  
Average Length ◽  
Flavonoid Biosynthesis ◽  
Full Length ◽  
Marker Assisted Breeding ◽  
Pacbio Rs Ii ◽  
Secondary Metabolite Biosynthesis ◽  
Non Coding Rnas ◽  
First Time ◽  
Flavonoid Biosynthesis Pathway ◽  
Simple Sequence

One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.

scholarly journals MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization

2018 ◽  
Author(s):  
Guanliang Meng ◽  
Yiyuan Li ◽  
Chentao Yang ◽  
Shanlin Liu
Keyword(s):  
Mitochondrial Genome ◽  
Open Source Software ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Ecological Studies ◽  
Free Open Source Software ◽  
Sequencing Technologies ◽  
Evolutionary Studies ◽  
Free Open Source

AbstractMitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules ofde novoassembly, findMitoScaf, annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available athttps://github.com/linzhi2013/MitoZ.

scholarly journals First Report of a Complete Genome Sequence of White spot syndrome virus from India

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
K. Vinaya Kumar ◽  
M. S. Shekhar ◽  
S. K. Otta ◽  
K. Karthic ◽  
J. Ashok Kumar ◽  
...  
Keyword(s):  
White Spot Syndrome Virus ◽  
De Novo ◽  
Economic Loss ◽  
White Spot ◽  
Nanopore Sequencing ◽  
Content Type ◽  
Sequencing Technologies ◽  
Aquaculture Industry ◽  
White Spot Syndrome ◽  
First Time

ABSTRACT White spot syndrome virus is a major pathogen of shrimp, causing economic loss to the aquaculture industry. For the first time, a complete de novo genome of an Indian isolate of this virus has been deciphered using Illumina and Nanopore sequencing technologies. The genome has 280,591 bp with 442 predicted coding genes.

scholarly journals Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 411 ◽  
Author(s):  
Yu Ge ◽  
Lin Tan ◽  
Bin Wu ◽  
Tao Wang ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
High Throughput Sequencing ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Persea Americana ◽  
Illumina Hiseq ◽  
Ssr Loci ◽  
Ssr Development

Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.

scholarly journals Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila

2017 ◽  
Vol 152 (4) ◽  
pp. 204-212 ◽  
Author(s):  
Lin Kang ◽  
Phillip George ◽  
Donald K. Price ◽  
Igor Sharakhov ◽  
Pawel Michalak
Keyword(s):  
Laser Capture Microdissection ◽  
De Novo ◽  
Chromosome Mapping ◽  
Drosophila Species ◽  
Sequencing Technologies ◽  
Physical Maps ◽  
New Information ◽  
Genome Assemblies ◽  
First Time ◽  
Laser Capture

Next-generation sequencing technologies have led to a decreased cost and an increased throughput in genome sequencing. Yet, many genome assemblies based on short sequencing reads have been assembled only to the scaffold level due to the lack of sufficient chromosome mapping information. Traditional ways of mapping scaffolds to chromosomes require a large amount of laboratory work and time to generate genetic and/or physical maps. To address this problem, we conducted a rapid technique which uses laser capture microdissection and enables mapping scaffolds of de novo genome assemblies directly to chromosomes in Hawaiian picture-winged Drosophila. We isolated and sequenced intact chromosome arms from larvae of D. differens. By mapping the reads of each chromosome to the recently assembled scaffolds from 3 Hawaiian picture-winged Drosophila species, at least 67% of the scaffolds were successfully assigned to chromosome arms. Even though the scaffolds are not ordered within a chromosome, the fast-generated chromosome information allows for chromosome-related analyses after genome assembling. We utilize this new information to test the faster-X evolution effect for the first time in these Hawaiian picture-winged Drosophila species.

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