Comparative Analysis of Chloroplast Genomes of Thalassiosira Species

Kuiyan Liu,Yang Chen,Zongmei Cui,Qing Xu,Nansheng Chen,Shuya Liu

doi:10.3389/fmars.2021.788307

Abstract

Thalassiosira is a species-rich genus in Bacillariophyta with important ecological contribution to primary productivity but can also pose negative impact on ecology by developing harmful algal blooms (HABs). However, genomic resources of only a few Thalassiosira species are currently available. Here, we constructed complete chloroplast genomes (cpDNAs) of six Thalassiosira strains (representing six Thalassiosira species T. rotula, T. profunda, T. nordenskioeldii, T. tenera, T. weissflogii, and Thalassiosira sp.), and compared them with published cpDNAs of other diatoms. Comparative analysis revealed that Thalassiosira cpDNAs have generally conventional and conserved quadripartite structure with important exceptions. Gene orders of cpDNAs of Thalassiosira sp. (CNS00561) and T. oceanica were different from that of other Thalassiosira species. Additionally, endosymbiotic gene transfers (EGT) were found to occur in the evolution of Thalassiosira cpDNAs. Furthermore, genomic regions of cpDNAs were found to be highly variable, which could be used to construct molecular markers for distinguishing Thalassiosira species with high resolution and high specificity. This study also demonstrated that Thalassiosira species emerged roughly around 51 MYA and diversified 17–28 MYA. Thalassiosira cpDNAs are not only valuable as super-barcode for phylogenetic analysis, but also important for functional and evolutionary analysis of diatoms.

Highlights

Thalassiosira (Mediophyceae, Bacillariophyta) is a species-rich genus with 287 recorded species, of which 175 have been officially accepted (Guiry and Guiry, 2021)
Six candidate Thalassiosira strains (CNS00050, CNS00051, CNS00052, CNS00472, CNS00439, and CNS00561) were characterized based on their morphological features (Figure 1B). Similarity of their molecular marker sequences to known Thalassiosira species were used for species annotation (Figure 1C and Supplementary Figure 1)
The annotation of the strain CNS00051 as T. rotula was supported by the high similarities of its 28S rDNA D1–D2, ITS, 16S rDNA, and rbcL to their corresponding reference sequences (Alverson et al, 2007; Kooistra et al, 2008; Supplementary Figure 1)

Summary

Introduction

Thalassiosira (Mediophyceae, Bacillariophyta) is a species-rich genus with 287 recorded species, of which 175 have been officially accepted (Guiry and Guiry, 2021). Most of these Thalassiosira species are considered to be cosmopolitan marine species, with only a few found in both fresh and brackish waters (Hasle, 1978; Hasle and Lange, 1989; Round et al, 1990). 54 Thalassiosira species and six varieties have been recorded (Gao and Cheng, 1992; Li et al, 2008a,b, 2013; Guo et al, 2018a,b). Some Thalassiosira species including T. weissflogii have been used as water quality indicators (Morelli et al, 2009; Araujo and Souza-Santos, 2013) and some are often used in nano-materials research (Losic et al, 2007; Pérez-Cabero et al, 2008)

Methods

Results

Discussion

Conclusion