Comparative Analysis of Chloroplast Genomes of Thalassiosira Species

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.

Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity

“…Syntenic analysis of the three Thalassionema species, as well as the pairwise comparison of these three species, all exhibited substantial genome rearrangement events (Fig. 9 ), which was different from previous studies that revealed strong collinearity among the cpDNAs of the same genus [ 47 , 48 ].

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“…The cpDNAs of different species T. bacillare , T. frauenfeldii and T. nitzschioides varied substantially in the length, ranging from 124,127 bp to 140,121 bp (Fig. 3 , Table 1 ), which is also expected because the lengths of cpDNAs of different species in the same genus can be quite different, such as in genera Thalassiosira and Pseudo-nitzschia [ 48 , 52 ], although cpDNAs of different species within a genus can be remarkably similar such as in genera Skeletonema and Chaetoceros [ 47 , 53 ]. According to previous studies, diatom cpDNAs are particularly labile in size, with the longest cpDNA being 201,816 bp in Plagiogramma staurophorum (MG755792) [ 18 ], and the smallest one being only 111,539 bp in Pseudo-nitzschia multiseries (KR709240) [ 54 ].…”

“…Diatom cpDNAs appear to be highly rearranged, even between close relatives [ 57 , 60 ]. Although in some diatom genera cpDNAs of different species revealed strong collinearity [ 47 , 48 ], we discovered substantial genome rearrangement events in cpDNAs of all three Thalassionema species constructed in this project (Fig. 9 ).…”

Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics

“…Complete plastome sequences of six coscinodiscophycean diatom species which exhibited rich diversity in cell morphology and cell size ( Figure 1 ) were successfully assembled. These plastomes ranged in size from 120.5 kb in A. curvatulus to 135.8 kb in S. turris , and their G + C content was from 30.37% in S. turris to 32.39% in G. delicatula ( Table 1 ), which were in the range of reported diatom plastomes ( Ruck et al, 2017 ; Liu et al, 2021a , b ; He et al, 2022 ; Wang et al, 2022 ). Similar to the reported diatom plastomes (e.g., Kowallik et al, 1995 ; Oudot-Le Secq et al, 2007 ; Tanaka et al, 2011 ; Hamsher et al, 2019 ), these newly assembled plastomes were mapped as canonical circular quadripartite structures with two IRs separating LSC and SSC.…”

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation

“…The genus Nitzschia exhibited highly diverse cpDNA genome arrangements, which was different from many diatom genera including Thalassiosira , Chaetoceros , and Skeletonema , in which the cpDNA genome exhibited high consistency [ 83 , 84 , 85 ]. The genus Cylindrotheca consisted of a small group of marine diatoms, with a few species described, including the existence of cryptic species, such as Cylindrotheca closterium [ 60 , 86 , 87 ].…”