Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Lou, Fangrui; Song, Na; Han, Zhiqiang; Gao, Tianxiang

doi:10.1016/j.ijbiomac.2020.01.029

Cited by 15 publications

(14 citation statements)

References 38 publications

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“…Genomes and transcriptomes from different HSC species (L. polyphemus, T. tridentatus, and C. rotundicauda) have been described previously (Ding et al 2005;Battelle et al 2016;Chen et al 2016;Chesmore et al 2016;Gong et al 2019;Liao et al 2019;Lou et al 2020;Shingate et al 2020;Zhou et al 2020). However, information about the genome of T. gigas has been scarce, which has limited the knowledge on the biology of this species.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA sequence of the horseshoe crabTachypleus gigas

Sarmiento

Chin

Lau

et al. 2021

Mitochondrial DNA Part B

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This paper reports on the complete mitochondrial (mt) genome of a horseshoe crab, Tachypleus gigas (T. gigas), in Kuala Kemaman, Terengganu, Malaysia. Whole-genome sequencing of hemocyte DNA was performed with Illumina HiSeq system and the generated reads were de novo assembled with ABySS 2.1.5 and reassembled using mitoZ against Carcinoscorpius rotundicauda and Limulus polyphemus, resulting in a contig of 15 Kb. Phylogenetic analysis of the assembled mt genome suggests that the Tachypleus gigas is closely related to Tachypleus tridentatus than to Carcinoscorpius rotundicauda.

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Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA sequence of the horseshoe crabTachypleus gigas

Sarmiento

Chin

Lau

et al. 2021

Mitochondrial DNA Part B

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“…Since 2002, ZMWs have been widely used for a large range of biophysical and biochemical applications, including DNA sequencing [234,235], enzymatic reaction monitoring [236,237], studying protein-protein interactions [238,239], nanopore sensing [240,241], and FRET [242][243][244]. In particular, single-molecule sequencing technology is commercialized by Pacific Biosystems as single-molecule real-time (SMRT) DNA sequencing [245][246][247][248]. Single-molecule sequencing uses fluorescent dNTPs phospholinked by four different colored fluorophores.…”

Section: Single-molecule Imaging Based On Zero-mode Waveguides (Zmws)mentioning

confidence: 99%

DNA Manipulation and Single-Molecule Imaging

2021

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DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

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“…Although the published genome has enriched the genetic information database of R. typus, the researchers predicted the incomplete protein-coding genes of R. typus only based on two published candidate gene sets (Stanke and Morgenstern, 2005;Haas et al, 2008). Meanwhile, the low completeness of R. typus genome annotation information also due to the lack of transcript data (Lou et al, 2020). Short transcripts were usually applied to the early genome annotation (Ozsolak and Milos, 2011;Duitama et al, 2012), but it is undeniable that the short transcripts have deficient in the recognition of alternative splicing, alternative transcription initiation or alternative transcription termination sites (Steijger et al, 2013;Tilgner et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…The third generation sequencing technology has revolutionized the genome annotation due to fulllength (FL) transcripts can be obtained to remedy the deficiency of short transcripts (Li et al, 2018). To date, FL transcripts has been successfully used to perfect the genome annotation information of many animals, such as Tachypleus tridentatus (Lou et al, 2020), Sus scrofa (Li et al, 2018), Danio rerio (Nudelman et al, 2018). Therefore, we have every reason to believe that FL transcripts will contribute to high-resolution R. typus genome annotation and provide an impeccable information for further elaboration of R. typus biology.…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome of the Whale Shark (Rhincodon typus) Facilitates the Genome Information

Lou

Wang

et al. 2022

Front. Mar. Sci.

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Rhincodon typus is a keystone and indicator species in marine ecosystems. Meanwhile, R. typus has been listed on the IUCN red list of vulnerable species. Here we used ONT platform to determine the full-length (FL) transcriptome of R. typus and obtained 14,930 FL transcripts. Among all FL transcripts, 14,915 transcripts were covered 11,892 genetic loci and 1,642 novel genetic loci were further found. Meanwhile, we identified 714 novel transcripts by compared FL transcripts with the R. typus genome. Based on FL transcripts, we also predicted the distribution patterns of ASs, LncRNAs, polyAs, CDSs and methylation sites on FL transcriptome of R. typus. Furthermore, a total of 31,021 (97.86%) CDSs can obtained annotation information. Overall, our work firstly provided the FL transcriptome and these sequences complete the annotated R. typus genome information. Furthermore, these information are a potential resource to study biological processes of R. typus.

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Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Cited by 15 publications

References 38 publications

Mitochondrial DNA sequence of the horseshoe crabTachypleus gigas

Mitochondrial DNA sequence of the horseshoe crabTachypleus gigas

DNA Manipulation and Single-Molecule Imaging

Full-Length Transcriptome of the Whale Shark (Rhincodon typus) Facilitates the Genome Information

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