Search

The clam Coelomactra antiquata (Spengler, 1802) is one of the most economically important marine bivalves in China. Previous genetic analysis shows that C. antiquata possibly consists of two cryptic species, a northern and a southern lineage. Some differences between the two lineages are observed in their morphology and fitness in aquaculture. However, little is known about the genetic basis of these differences. In this study, a comparative transcriptomics study was performed to provide additional information for delineating the cryptic species of C. antiquata, as well as insights into the adaptive evolution in the southern lineage of C. antiquata. A total of 4377 orthologous genes were identified using a phylogenetic tree-based approach. The Kimura 2-parameter genetic distances were 0.0385 between the two lineages of C. antiquata, and 0.006 within the northern lineage. The sequence divergences supports that the lineages represent two cryptic species. We identified 28 positively selected genes (PSGs) from the southern lineage of C. antiquata using a modified branch-site model. The PSGs were implicated in innate immune responses, metabolism, development, cell division, transmembrane transport, and signaling processes, which could be related to the higher disease resistance, growth rate, and adaptability of the southern lineage than its northern counterpart. The comparative transcriptome analysis provides a foundation for future investigations on the biological differences between the two lineages of C. antiquata.

Background Crustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of crustacean aquaculture and biodiversity loss, understanding the gene regulatory mechanisms of growth, reproduction, and development of crustaceans is crucial to both aquaculture development and biodiversity conservation of this group of organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating gene expression. However, crustacean transcription factors are still largely unknown, because the lack of complete genome sequences of most crustacean species hampers the studies on their transcriptional regulation on a system-wide scale. Thus, the current TF databases derived from genome sequences contain TF information for only a few crustacean species and are insufficient to elucidate the transcriptional diversity of such a large animal group. Results Our database CrusTF (http://qinlab.sls.cuhk.edu.hk/CrusTF) provides comprehensive information for evolutionary and functional studies on the crustacean transcriptional regulatory system. CrusTF fills the knowledge gap of transcriptional regulation in crustaceans by exploring publicly available and newly sequenced transcriptomes of 170 crustacean species and identifying 131,941 TFs within 63 TF families. CrusTF features three categories of information: sequence, function, and evolution of crustacean TFs. The database enables searching, browsing and downloading of crustacean TF sequences. CrusTF infers DNA binding motifs of crustacean TFs, thus facilitating the users to predict potential downstream TF targets. The database also presents evolutionary analyses of crustacean TFs, which improve our understanding of the evolution of transcriptional regulatory systems in crustaceans. Conclusions Given the importance of TF information in evolutionary and functional studies on transcriptional regulatory systems of crustaceans, this database will constitute a key resource for the research community of crustacean biology and evolutionary biology. Moreover, CrusTF serves as a model for the construction of TF database derived from transcriptome data. A similar approach could be applied to other groups of organisms, for which transcriptomes are more readily available than genomes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4305-2) contains supplementary material, which is available to authorized users.

Identification methods of collagens and gelatins have been studied many years due to religious and food safety issues. Some researchers detected the collagen while others took up their study based on DNA at the first time. In this work, we used a closed-tube loop-mediated isothermal amplification (LAMP) technique to differentiate collagen and gelatin samples. DNA was extracted by DNeasy mericon Food Kit and was dissolved in 30 µl elution buffer, optimum concentration of Mg2+, deoxyribonucleoside triphosphates(dNTPs), betaine in LAMP reaction is 6.0 mmol/L, 2.0 mmol/L, and 0.8 mmol/L, respectively. After LAMP reaction, samples being detected changed their initial color to green, others’ were colorless or brown slightly. The research offered a simple, fast detection technique to differentiate collagen and gelatin samples derived from porcine, bovine and channel catfish (Ictalurus punctatus) , the collagens’ species can be determined by color variation in reaction tubes within two hour.

Thalli of Porphyra yezoensis growing in the intertidal region periodically experience diverse abiotic stresses induced by tidal cycles. To investigate the contribution of 70-kDa heat shock proteins (HSP70s) to abiotic stress tolerance in P. yezoensis thalli, we isolated the cDNAs of two HSP70 genes (designated as PyHSP70-1 and PyHSP70-2) from P. yezoensis by in silico cloning and RT-PCR amplification, and examined their relative mRNA expression levels in P. yezoensis thalli responding to various abiotic stresses using real-time quantitative PCR. The deduced amino acid sequences of the two PyHSP70s lacked signal peptides, but contained signature motifs and conserved domains of the HSP70 family. The two PyHSP70s shared high amino acid sequence similarities with cytosolic HSP70s from other algae and higher plants, and clustered together with all cytosolic HSP70s in the phylogenetic tree, indicating they belong to the cytosolic HSP70 family. Expression of the two PyHSP70 genes was induced by cold shock at 0°C and heat shocks at 20°C and 25°C, and was significantly upregulated in a dose-dependent manner. The expression patterns under heat shock, along with the absence of introns in the coding regions, demonstrate that the two PyHSP70s are inducible HSP70s. Expression of the two PyHSP70 genes was repressed by desiccation stress, suggesting that they do not play a role in tolerance to desiccation stress. The expression patterns in response to salinity stress were different between PyHSP70-1 and PyHSP70-2 genes. The expression of PyHsp70-1 was induced by a salinity of 5; however, the expression of PyHsp70-2 was induced by salinities of 35 and 45. The different expression patterns suggest that they have distinct biological tasks.

Background Porphyra yezoensis Ueda is one of the most important edible seaweed, with a dimorphic life cycle which consists of gametophyte as macroscopical blade and sporophyte as microscopic filamentous. Conspicuous differences exist in the two generations, such as morphology, cell structure, biochemistry, physiology, and so on. The developmental process of Porphyra yezoensis has been studied thoroughly, but the mechanism is still ambiguous and few studies on genetic expression have been carried out. In this study, the suppression subtractive hybridization (SSH) method conducted to generate large-scale expressed sequence tags (EST) is designed to identify gene candidates related to the morphological and physiological differences between the gametophytic and sporophytic generations of Porphyra yezoensis Ueda. Findings Each 300 clones of sporophyte and gametophyte cells were dipped onto the membrane for hybridization. The result of dot-blot suggested there were 222 positive clones in gametophyte library and 236 positive clones in sporophyte library. 383 positive clones of strongest signals had been sequenced, and 191 EST sequences of gametophyte and 192 of sporophyte were obtained. A total of 196 genes were obtained, within which 104 genes were identified from the gametophyte and 92 from the sporophyte. Thirty-nine genes of the gametophyte and 62 genes of the sporophyte showed sequence similarity to those genes with known or putative functions which were classified according to their putative biological roles and molecular functions. The GO annotation showed about 58% of the cellular component of sporophyte and gametophyte cells were mainly located in cytoplasm and nucleus. The special genes were located in Golgi apparatus, and high expression in plastid, ribosome and endoplasmic reticulum. The main biological functions of gametophyte cells contributed to DNA repair/replication, carbohydrate metabolism, transport and transcription, especially in response to heat and oxidative stress. The sporophyte cell expresses more genes in transcription, transport, carbohydrate metabolism, particularly in signal transduction, DNA and protein modification, protein and nucleotide metabolism. Four genes are expressed on both gametophyte and sporophyte cells and eighteen genes have not been annotated. Conclusion According to the information of GO annotation, the gametophyte tends to growth and self- protection while the sporophyte tends to be more active in development. Interpretation of the differentially expressed genes revealed new insights into the molecular processes of the generation alternation of Porphyra yezoensis. Further investigation are needed due to insufficiency of functional genes research and indeterminancy of the functions of many sequences.