Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes
β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms ow...
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| Format: | Article |
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MDPI AG
2021-07-01
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| Series: | Marine Drugs |
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| Online Access: | https://www.mdpi.com/1660-3397/19/7/392 |
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| author | Haomiao Cheng Chris Bowler Xiaohui Xing Vincent Bulone Zhanru Shao Delin Duan |
| author_facet | Haomiao Cheng Chris Bowler Xiaohui Xing Vincent Bulone Zhanru Shao Delin Duan |
| author_sort | Haomiao Cheng |
| collection | DOAJ |
| description | β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative <i>Thalassiosira</i> species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that <i>Thalassiosira weissflogii</i> was an appropriate candidate chitin producer. A full-length (FL) transcriptome of <i>T. weissflogii</i> was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate <i>T. weissflogii</i> molecular research and the exploitation of β-chitin-derived high-value enzymes and products. |
| first_indexed | 2024-03-10T09:34:28Z |
| format | Article |
| id | doaj.art-90c7a4f1531e44fb8ce4e170f686bcbd |
| institution | Directory Open Access Journal |
| issn | 1660-3397 |
| language | English |
| last_indexed | 2024-03-10T09:34:28Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Marine Drugs |
| spelling | doaj.art-90c7a4f1531e44fb8ce4e170f686bcbd2023-11-22T04:14:16ZengMDPI AGMarine Drugs1660-33972021-07-0119739210.3390/md19070392Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related GenesHaomiao Cheng0Chris Bowler1Xiaohui Xing2Vincent Bulone3Zhanru Shao4Delin Duan5CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaInstitut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, FranceDivision of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, SwedenDivision of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, SwedenCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Chinaβ-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative <i>Thalassiosira</i> species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that <i>Thalassiosira weissflogii</i> was an appropriate candidate chitin producer. A full-length (FL) transcriptome of <i>T. weissflogii</i> was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate <i>T. weissflogii</i> molecular research and the exploitation of β-chitin-derived high-value enzymes and products.https://www.mdpi.com/1660-3397/19/7/392PacBio sequencingfull-length transcriptome<i>Thalassiosira weissflogii</i>chitinchitosan |
| spellingShingle | Haomiao Cheng Chris Bowler Xiaohui Xing Vincent Bulone Zhanru Shao Delin Duan Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes Marine Drugs PacBio sequencing full-length transcriptome <i>Thalassiosira weissflogii</i> chitin chitosan |
| title | Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes |
| title_full | Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes |
| title_fullStr | Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes |
| title_full_unstemmed | Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes |
| title_short | Full-Length Transcriptome of <i>Thalassiosira</i> <i>weissflogii</i> as a Reference Resource and Mining of Chitin-Related Genes |
| title_sort | full length transcriptome of i thalassiosira i i weissflogii i as a reference resource and mining of chitin related genes |
| topic | PacBio sequencing full-length transcriptome <i>Thalassiosira weissflogii</i> chitin chitosan |
| url | https://www.mdpi.com/1660-3397/19/7/392 |
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