Identification and expression of cysteine sulfite decarboxylase genes and their response to hyposalinity stress in Ruditapes philippinarum

Cysteine sulfinate decarboxylase (CSAD) is a rate-limiting enzyme in taurine biosynthesis. In this study, the structure and expression characteristics of the RpCSAD gene in Ruditapes philippinarum were analyzed. The pyridoxal phosphate (PLP)-dependent amino acid carboxylase structural domains and catalytic active sites of six copies of RpCSAD were highly conserved. Tissue expression analysis demonstrated that RpCSAD1 and RpCSAD3-6 was primarily expressed in the mantle tissue, and RpCSAD2 in the water tube and gonad tissue. After exposure to hyposalinity stress, the expression levels of RpCSADs were found to be upregulated in all three shell-colored groups of clams. Remarkably, there was a pronounced increase in the expression of RpCSAD1-6 observed specifically in the zebra shell-color groups. These findings strongly suggest the involvement of taurine metabolism in the response of zebra shell-color clams to low salinity stress, thereby emphasizing its critical role in the adaptation mechanisms. These findings could contribute to a better understanding the mechanisms of osmotic stress tolerance in shellfish

Draft genome sequence of the mulberry tree Morus notabilis

Human utilization of the mulberry–silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species’ spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant–herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants

Seawater acidification affects the physiological energetics and spawning capacity of the Manila clam Ruditapes philippinarum during gonadal maturation

Ocean acidification is predicted to have widespread implications for marine bivalve mollusks. While our understanding of its impact on their physiological and behavioral responses is increasing, little is known about their reproductive responses under future scenarios of anthropogenic climate change. In this study, we examined the physiological energetics of the Manila clam Ruditapes philippinarum exposed to CO2-induced seawater acidification during gonadal maturation. Three recirculating systems filled with 600 L of seawater were manipulated to three pH levels (8.0, 7.7, and 7.4) corresponding to control and projected pH levels for 2100 and 2300. In each system, temperature was gradually increased ca. 0.3 °C per day from 10 to 20 °C for 30 days and maintained at 20 °C for the following 40 days. Irrespective of seawater pH levels, clearance rate (CR), respiration rate (RR), ammonia excretion rate (ER), and scope for growth (SFG) increased after a 30-day stepwise warming protocol. When seawater pH was reduced, CR, ratio of oxygen to nitrogen, and SFG significantly decreased concurrently, whereas ammonia ER increased. RR was virtually unaffected under acidified conditions. Neither temperature nor acidification showed a significant effect on food absorption efficiency. Our findings indicate that energy is allocated away from reproduction under reduced seawater pH, potentially resulting in an impaired or suppressed reproductive function. This interpretation is based on the fact that spawning was induced in only 56% of the clams grown at pH 7.4. Seawater acidification can therefore potentially impair the physiological energetics and spawning capacity of R. philippinarum

Growth performance and biochemical composition of the oysters Crassostrea sikamea, Crassostrea angulata and their hybrids in southern China

The Kumamoto oyster (Crassostrea sikamea) and the Portuguese oyster (C.angulata) are important aquaculture species which naturally coexist along the southern coast of China. To understand the potential feasibility of hybridization between the two species, we conducted two-by-two factorial cross-experiments in Beihai (Guangxi province), and also compared the survival and growth of the hybrids to that of the two parental progenies during the grow-out period from July 2014 to July 2015. Genetic analysis confirmed that the hybrid spats were true hybrids. Additionally, the biochemical composition of the 1-year-old oyster progenies was determined. In July 2015, the mean shell height of the hybrids was 42.98 +/- 6.29mm, which was higher than that of the Kumamoto oyster progeny. The cumulative survival rate of the hybrids was 26.37 +/- 1.32%, which was higher than that of the progeny of the Portuguese oyster. Mean lipid content of the hybrids was 13.65 +/- 1.63% of dry weight, which showed obvious heterosis compared to those of the two parental progenies. Observation of gonads revealed that all hybrids were completely fertile. Furthermore, relative expression of the lipid homeostasis genes, SREBP (sterol regulatory element-binding proteins), PPAR (peroxisome proliferator-activated receptor) and INSIG (insulin-induced gene) were found to vary between parental progenies and the hybrids, thus providing a possible reason for difference in the lipid contents of these experimental groups. Overall, the hybrids were viable, rich in lipid and completely fertile and thus could serve as a promising aquaculture stock for oyster breeding in southern China

Stress levels over time in Ruditapes philippinarum: The effects of hypoxia and cold stress on hsp70 gene expression

Ruditapes philippinarum is one of the most commercially important marine bivalves worldwide with a production over 4.0 million tons and 3.7 million USD in 2015. The Manila clam displays different shell color strains (white, zebra, and orange) in its natural habitat. Heat shock proteins (HSPs) play significant roles in response to adverse environmental stresses in aquatic animals. In this study, the expression levels of HSP70 gene were analyzed by qPCR in gills of Manila clams under hypoxia and cold stresses. The expression pattern of HSP70 was observed in different color strains of Manila clam under low temperature challenge. The expression of HSP70 was up-regulated significantly up to 8 days in cultured Manila clam under hypoxia stress. HSP70 expression in gill was inducible under hypoxia and low temperature stress. These findings contribute to our better understanding of the molecular response and biological function of HSPs in defending against low temperature and hypoxia challenges in R. philippinarum. Keywords: Ruditapes philippinarum, Heat shock protein 70, Expression profile, Low temperature, Hypoxi

Molecular cloning and expression analysis of tyrosinases (tyr) in four shell-color strains of Manila clam Ruditapes philippinarum

The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum

Additional file 6 of Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum)

Additional file 6

Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model

Abstract Background Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. Results In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. Conclusion This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica