Insights into cryptic diversity and adaptive evolution of the clam Coelomactra antiquata (Spengler, 1802) from comparative transcriptomics

Liu, Yi; Yan, Ka; Qin, Jing; Chu, Ka Hou; Shen, Xin; Meng, Xianhong

doi:10.1007/s12526-019-00964-w

Cited by 3 publications

(3 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…By processing and analyzing the sequenced data, a total of 39,209 unigenes were finally identified, with an average length of 2,732 bp. In previous studies, some researchers used the Illumina platform to sequence the transcriptome, and obtained the second-generation transcriptome data of the C. antiquata ( Yi et al, 2019 ). The second-generation sequencing identified 214,732 unigenes with a mean length of 616.2 bp.…”

Section: Discussionmentioning

confidence: 99%

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.

show abstract

Section: Discussionmentioning

confidence: 99%

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…This gene encodes the first and rate‐limiting enzyme in the hexosamine biosynthetic pathway, a glucose metabolism pathway that results in the synthesis of a nucleotide sugar UDP‐GlcNAc. This sugar is subsequently used for the post‐translational modification of intracellular proteins that regulate nutrient sensing and stress response (Yamazaki, 2014; Yi et al, 2019). Ribosomal genes were also expressed at a higher level (Figure 4g,h) compared to those exposed to ambient pH, including the genes Rps8 and Rps4x (average log 2 FC in order: 2.03, 2.00, see Table S4).…”

Section: Resultsmentioning

confidence: 99%

“…This gene encodes the first and rate-limiting enzyme in the hexosamine biosynthetic pathway, a glucose metabolism pathway that results in the synthesis of a nucleotide sugar UDP-GlcNAc. This sugar is subsequently used for the post-translational modification of intracellular proteins that regulate nutrient sensing and stress response (Yamazaki, 2014;Yi et al, 2019). Ribosomal genes were also F I G U R E 2 Logarithmic fold enrichment of GO terms after gene list overrepresentation enrichment analysis with genes differentially expressed in the four clusters (Table S2, FDR < 0.05).…”

Section: Differential Gene Expression Between Ph Treatmentsmentioning

confidence: 99%

Parentage influence on gene expression under acidification revealed through single‐embryo sequencing

Fung,

Chau,

Tong

et al. 2023

Molecular Ecology

View full text Add to dashboard Cite

The dissolution of anthropogenic carbon dioxide (CO2) in seawater has altered its carbonate chemistry in the process of ocean acidification (OA). OA affects the viability of marine species. In particular, calcifying organisms and their early planktonic larval stages are considered vulnerable. These organisms often utilize energy reserves for metabolism rather than growth and calcification as supported by bulk RNA‐sequencing (RNA‐seq) experiments. Yet, transcriptomic profiling of a bulk sample reflects the average gene expression of the population, neglecting the variations between individuals, which forms the basis for natural selection. Here, we used single‐embryo RNA‐seq on larval sea urchin Heliocidaris crassispina, which is a commercially and ecologically valuable species in East Asia, to document gene expression changes to OA at an individual and family level. Three paternal half‐sibs groups were fertilized and exposed to 3 pH conditions (ambient pH 8.0, 7.7 and 7.4) for 12 h prior to sequencing and oxygen consumption assay. The resulting transcriptomic profile of all embryos can be distinguished into four clusters, with differences in gene expressions that govern biomineralization, cell differentiation and patterning, as well as metabolism. While these responses were influenced by pH conditions, the male identities also had an effect. Specifically, a regression model and goodness of fit tests indicated a significant interaction between sire and pH on the probability of embryo membership in different clusters of gene expression. The single‐embryo RNA‐seq approach is promising in climate stressor research because not only does it highlight potential impacts before phenotypic changes were observed, but it also highlights variations between individuals and lineages, thus enabling a better determination of evolutionary potential.

show abstract

Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications

Liu

Wang

et al. 2023

International Journal of Biological Macromolecules

View full text Add to dashboard Cite

Insights into cryptic diversity and adaptive evolution of the clam Coelomactra antiquata (Spengler, 1802) from comparative transcriptomics

Cited by 3 publications

References 73 publications

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Parentage influence on gene expression under acidification revealed through single‐embryo sequencing

Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications

Contact Info

Product

Resources

About