Full-Length Transcriptome of Thalassiosiraweissflogii as a Reference Resource and Mining of Chitin-Related Genes.

Xiaohui Xing,Zhanru Shao,Delin Duan,Vincent Bulone,Chris Bowler,Haomiao Cheng

doi:10.3390/md19070392

Abstract

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 Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii 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 T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

Highlights

Chitin, a polymer of 1,4-linked β-D-N-acetylglucosaminyl residues, is the second most abundant natural biopolymer after cellulose, and is widely distributed across taxa [1,2,3]
We found that all four diatom species harbour rather complete chitin metabolism pathways (Figure 7)
In T. weissflogii, chitinases accounted for over half of the sum (53.0%), indicating the presence of an active chitin degradation process

Summary

Introduction

A polymer of 1,4-linked β-D-N-acetylglucosaminyl residues, is the second most abundant natural biopolymer after cellulose, and is widely distributed across taxa [1,2,3]. Together with its partially de-N-acetylated derivative chitosan, chitin has many biomedical applications, such as wound healing, artificial organs and drug delivery [4]. There are very few classes of organisms that produce β-chitin, such as the diatom Thalassiosira sp. Various diatoms have been previously reported to produce chitin, mainly in the genera Thalassiosira and Cyclotella [10,11]. 2 of 14 2 of 13 been previously reported to produce chitin, mainly in the genera Thalassiosira and Cy‐ rceloptoelrltao[f10th,1e1o].cTcuhrerefnircset orefpcohritinofinthdeiaotcocmursrwenacseinofTc.hwiteinssflinogdiiia(fltoumvisatwilias)s, iwnhTic. hwseihsosfwloegdii t(hflautvTia.twiliesi)s,sflwohgiicchhsithinowreepdretsheantteTd. wupeistsofl3o4g%ii cohfitthine troetparlecseellnmteadssu(pintcolu3d4%ingotfhtehseiltioctaa)l[c1e2l]l.

Results and Discussion

Annotation Analyses

Analyses of Alternative Splicing and Simple Sequence Repeats

Chitin-Related Gene Mining

Library Construction and Sequencing

Data Processing

Functional Annotation

Detection of Alternative Splicing and Simple Sequence Repeats

Mining of Chitin Metabolism Genes in Diatoms

Conclusions