Genome-wide identification and structural analysis of heat shock protein gene families in the marine rotifer Brachionus spp.: Potential application in molecular ecotoxicology

Park, Jun Chul; Kim, Duck-Hyun; Lee, Yoseop; Lee, Min Chul; Kim, Tai Kyoung; Yim, Joung Han; Lee, Jae‐Seong

doi:10.1016/j.cbd.2020.100749

Cited by 6 publications

(3 citation statements)

References 127 publications

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“…The transcriptional expansion of this gene family may be of interest due to its involvement in many cellular processes, including cell cycle control, cell survival, hormones, and other signaling pathways (Jackson, 2013). The HSP gene family results of the K. kelletii genome are comparable to those in other molluscan genomes (Park et al, 2020;Nong et al, 2022). Our genome results are also congruent with previous research indicating an expansion of the HSP70 gene family between Gastropod and Bivalve genomes (Zhang et al, 2012;Takeuchi et al, 2016;Guerin et al, 2019;Nong et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion

Daniels,

Andrasz,

Zarate

et al. 2023

Front. Mar. Sci.

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Understanding the genomic characteristics of non-model organisms can bridge research gaps between ecology and evolution. However, the lack of a reference genome and transcriptome for these species makes their study challenging. Here, we complete the first full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii, a marine gastropod exhibiting a poleward range expansion coincident with climate change. We used a combination of Oxford Nanopore Technologies, PacBio, and Illumina sequencing platforms and integrated a set of bioinformatic pipelines to create the most complete and contiguous genome documented among the Buccinoidea superfamily to date. Genome validation revealed relatively high completeness with low missing metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) and an average coverage of ∼70x for all contigs. Genome annotation identified a large number of protein-coding genes similar to some other closely related species, suggesting the presence of a complex genome structure. Transcriptome assembly and analysis of individuals during their period of peak embryonic development revealed highly expressed genes associated with specific Gene Ontology (GO) terms and metabolic pathways, most notably lipid, carbohydrate, glycan, and phospholipid metabolism. We also identified numerous heat shock proteins (HSPs) in the transcriptome and genome that may be related to coping with thermal stress during the sessile life history stage. A robust reference genome and transcriptome for the non-model organism K. kelletii provide resources to enhance our understanding of its ecology and evolution and potential mechanisms of range expansion for marine species facing environmental changes.

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Section: Discussionmentioning

confidence: 99%

De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion

Daniels,

Andrasz,

Zarate

et al. 2023

Front. Mar. Sci.

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“…The utilization of available transcriptomes and different expression patterns of B. calyci orus s.s. and B. fernandoi allowed us to identify a candidate gene which likely plays a role in the differences in temperature adaptation among the two Brachionus species. Indeed, HSPs have been shown to be involved in the response to various environmental stressors such as thermal stress, toxins, oxidative conditions (Mahmood et al, 2014;Park et al, 2020;Santoro, 1999), and aging (Yang et al, 2014). The importance of HSPs in the process of thermotolerance for invertebrates, particularly HSP 40kDa, HSP 60kDa and HSP 70kDa, was previously shown by Smith et al (2012) in the monogonont rotifer B. manjavacas.…”

Section: Candidate Gene Selection Pipelinementioning

confidence: 96%

Variation in Heat Shock Protein 40kDa relates to divergence in thermotolerance among cryptic rotifer species

Kiemel

Gurke

Paraskevopoulou

et al. 2022

Preprint

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Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40kDa) which exhibits cross species pronounced structural variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.

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“…Notably, intertidal sediments generally act as important sinks for pollutants in coastal environments [ 16 , 17 ]. Recently, growing evidence has confirmed the importance of HSPs in response to various environmental pollutants and stressors [ 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. Sulfide, a sum of H 2 S, HS − , and S 2− , is widely distributed in intertidal sediments.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)

Liu

Qin

Wei

et al. 2022

IJMS

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The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.

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Genome-wide identification and structural analysis of heat shock protein gene families in the marine rotifer Brachionus spp.: Potential application in molecular ecotoxicology

Cited by 6 publications

References 127 publications

De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion

De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion

Variation in Heat Shock Protein 40kDa relates to divergence in thermotolerance among cryptic rotifer species

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)

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