Draft Genome Assembly of a Fouling Barnacle, Amphibalanus amphitrite (Darwin, 1854): The First Reference Genome for Thecostraca

Kim, Jeehoon; Kim, Hyun Kyong; Kim, Hee‐Soo; Chan, Benny K. K.; Kang, Seunghyun; Kim, Won

doi:10.3389/fevo.2019.00465

Cited by 21 publications

(27 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Despite this progress, a large number of proteins in acorn barnacles do not share significant homology with any known proteins and, therefore, remain uncharacterized. The scope of this issue has been partly reduced with the publication of the genomes of a limited number of marine arthropods (Colbourne et al, 2011;Kao et al, 2016;Zhang et al, 2019) and, more recently, a draft genome of A. amphitrite itself (Kim et al, 2019). We note the other species are still relatively distant relatives and highlight the need for high-quality genomic sequencing in A. amphitrite.…”

Section: Discussionmentioning

confidence: 99%

Distribution of Select Cement Proteins in the Acorn Barnacle Amphibalanus amphitrite

et al. 2020

View full text Add to dashboard Cite

Acorn barnacles are major marine fouling organisms. Their success is largely due to an ability to adhere to diverse substrates via a sub-micron thick proteinaceous adhesive layer that develops as the organism molts and expands its base. Recent work has expanded the set of proteins identified within the adhesive interface, but one outstanding question concerns their spatial distribution throughout the organism. Here, we employ immunological analysis of Amphibalanus amphitrite tissue sections and identify the presence of two cement proteins, AaCP19-1 and AaCP43-1, in areas far removed from the adhesive interface. Confocal imaging reveals specific staining along different tissue linings of the organism as well as other non-cementing regions. Additionally, we employ a modified, pressure cycling technology approach to recover protein from histological tissue sections to perform proteomics analysis. Mass spectrometry analysis of proteins recovered from transverse histological sections of the upper portion of barnacles indicates the presence of these same proteins, complementing the immunostaining observations. The proteomics analysis also revealed the presence of other proteins first identified in the adhesive layer. While some proteins are clearly enriched at the surface interface, our findings challenge the concept that cement proteins are exclusive to the substrate interface and suggest they may have an expanded physiological role beyond substrate adhesion-related processes of A. amphitrite.

show abstract

Section: Discussionmentioning

confidence: 99%

Distribution of Select Cement Proteins in the Acorn Barnacle Amphibalanus amphitrite

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Despite their important roles in fouling communities, no species from the family Lepadidae has a sequenced genome. Within the whole infraclass Cirripedia, only the acorn barnacle Amphibalanus amphitrite (Balanidae) has a sequenced genome ( Kim et al., 2019 ). We conducted comparative genomic analyses with other pancrustacean lineages to understand barnacle genomic structures that are likely associated with their unique sessile life with particular emphasis on gene family expansion and contraction.…”

Section: Introductionmentioning

confidence: 99%

Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia)

Qiu

Chan

2021

Heliyon

View full text Add to dashboard Cite

Members of the infraclass Cirripedia, commonly called barnacles, are unique among the subphylum Crustacea in that they exhibit a biphasic life cycle with a planktonic larval stage and a sessile adult stage. Understanding their unique sessile life and mechanisms of attachment are hampered by the lack of genomic resources. Here, we present a 746 Mb genome assembly of Lepas anserifera – the first sequenced stalked barnacle genome. We estimate that Cirripedia first arose ~495 million years ago (MYA) and further diversified since Mesozoic. A demographic analysis revealed remarkable population changes of the barnacle in relation to sea-level fluctuations in the last 2 MYA. Comparative genomic analyses revealed the expansion of a number of developmental related genes families in barnacle genomes, such as Br–C, PCP20 and Lola, which are potentially important for the evolution of metamorphosis, cuticle development and central nervous system. Phylogenetic analysis and tissue expression profiling showed the possible roles of gene duplication, functional diversification and co-option in shaping the genomic evolution of barnacles. Overall, our study provides not only a valuable draft genome for comparative genomic analysis of crustacean evolution, but also facilitates studies of biofouling control.

show abstract

“…Preliminary differential expression analysis with DESeq2 (Love et al, 2014) revealed a small set of clusters that were exclusively expressed in three samples and that appeared to be of barnacle origin (>90% sequence similarity to barnacle transcripts, via blastx to the NCBI non redundant protein database). In order to identify and remove all barnacle clusters, minimap2 (Li, 2018) was used to map all transcripts to a genomic database consisting of the Porites lutea (Robbins et al, 2019), Cladocopium goreaui (Liu et al, 2018), and Amphibalanus amphitrite genomes (Kim et al, 2019). Mapping was performed using the xsplice option to allow gapped alignment and up to 10% sequence divergence.…”

Section: Rna Sequencing Assembly and Transcript Quantificationmentioning

confidence: 99%

The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective

et al. 2021

View full text Add to dashboard Cite

Competitive interactions shape coral assemblages and govern the dynamics of coral ecosystems. Although competition is an ecological concept, the outcomes of competitive interactions are ultimately determined by patterns of gene expression. These patterns are subject to genotypic variation on both sides of any interaction. Such variation is typically treated as “noise”, but it is sometimes possible to identify patterns within it that reveal important hidden factors in an experiment. To incorporate genotypic variation into the investigation of coral competitive interactions, we used RNA-sequencing to study changes in gene expression in a hard coral (Porites cylindrica) resulting from non-contact competition experiment with a soft coral (Lobophytum pauciflorum). Hard coral genotype explained the largest proportion of variation between samples; however, it was also possible to detect gene expression changes in 76 transcripts resulting from interaction with the soft coral. In addition, we found a group of 20 short secreted proteins that were expressed as a coordinated unit in three interacting Porites-Lobophytum pairs. The presence of this secretion response was idiosyncratic in that it could not be predicted based on polyp behaviour, or the genotype of hard or soft coral alone. This study illustrates the significance of individual variation as a determinant of competitive behaviour, and also provides some intriguing glimpses into the molecular mechanisms employed by hard corals competing at a distance.

show abstract

Draft Genome Assembly of a Fouling Barnacle, Amphibalanus amphitrite (Darwin, 1854): The First Reference Genome for Thecostraca

Cited by 21 publications

References 41 publications

Distribution of Select Cement Proteins in the Acorn Barnacle Amphibalanus amphitrite

Distribution of Select Cement Proteins in the Acorn Barnacle Amphibalanus amphitrite

Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia)

The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective

Contact Info

Product

Resources

About