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Background: Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. Methods and results: We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422 bp and 16,027 bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75 Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. Conclusions: Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae. [ABSTRACT FROM AUTHOR]

Simple Summary: Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. In this study, the complete mitochondrial genome of Mactra grandis was characterized for the first time. The newly sequenced mitochondrial genome fits the typical composition pattern of mollusks with 37 functional genes. Among the Mactridae species with reported mitochondrial genomes, Mactra grandis has the closest relationship with Mactra cygnus. The gene arrangement, genetic distance, and selective pressure of protein-coding genes among Mactra species were also analyzed. This study provides a molecular basis for taxonomy and germplasm research on Mactridae species. Mitochondrial genomes are playing an increasingly important role in molluscan taxonomy, germplasm, and evolution studies. The first complete mitochondrial genome of the commercial big brown mactra clam, Mactra grandis, was characterized using Illumina next-generation sequencing in this study. The 17,289 bp circular genome has a typical gene organization of 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, with an obvious (A + T)-bias of 64.54%. All PCGs exhibited a homogeneous bias in nucleotide composition with a (A + T)-bias, a positive GC skew, and a negative AT skew. Results of phylogenetic analysis showed that Mactra grandis was most closely related to Mactra cygnus. The functional gene arrangement of the two species was identical but different from other Mactra species. The congeneric relationships among Mactra species were demonstrated by genetic distance analysis. Additionally, the selective pressure analysis suggested that cox1 was highly efficient for discriminating closely related species in genus Mactra, while nad2 was the most appropriate marker for population genetic analysis. [ABSTRACT FROM AUTHOR]

The phylogeny of Veneridae has always been controversial. An inappropriate choice of morphological characteristics and loss of critical molecular information will inevitably lead to conflicts between morphological and molecular evolutionary inferences. Phylogenetic relationships in Veneridae, based on both multigene fragments and mitogenomes, were studied, including the redefinition of controversial taxa based on morphological characteristics. Our results support the monophyly of the subfamilies Chioninae, Gemminae, Gouldiinae, Petricolinae and Sunettinae. Callistinae and Pitarinae are considered as valid. The genus Placamen is placed in Dosiniinae, Periglypta in Venerinae, Pelecyora in Pitarinae and Lioconcha and Hyphantosoma in Gouldiinae. Anomalodiscus squamosus is assigned to Timoclea , whereas Marcia hiantina and Marcia japonica are placed in Tapes. In addition, Claudiconcha japonica is removed from Petricolinae, and Gafrarium tumidum is considered valid. Finally, we propose to divide Veneridae into two families: Veneridae s.s. and Meretricidae, constituted by four and 11 subfamilies, respectively. Our study verifies that multigene fragments and mitochondrial genomes are of vital importance in phylogenetic relationships within Veneridae. [ABSTRACT FROM AUTHOR]

Crossbreeding is an effective approach to manage the genetic decline in aquaculture. One-way hybrids of Crassostrea sikamea (♀) and Crassostrea gigas (♂) have advantages in growth traits and adaptation to high temperature. Here, we used high-throughput sequencing to analyze the molecular processes in the hybrids under and after thermal stress. The hybrids were cultured in the seawater with an increasing temperature from 25 °C to 40 °C during 10 hours, which is regarded as the thermal stress stage. Then the temperature decreased from 40 °C to 25 °C within 2 h, which is regarded as the recovery stage. In this study, 1293 significant differentially expressed genes (DEGs) were obtained under thermal stress, of which 576 were upregulated and 717 were downregulated, and 740 significant differentially expressed genes (DEGs) were obtained in the recovery stage, of which the number of upregulated and downregulated genes was 409 and 331, respectively. The antigen processing and presentation, NOD-like, and NF-kappa B pathways were significantly enriched during the thermal stress stage. The MAPK and PPAR signaling pathways were significantly enriched during the recovery stage. The HSP70, HSP90, and CANX genes were strongly and rapidly upregulated in the control/thermal stress groups but were slightly less upregulated in the thermal stress/recovery group. These results indicate that the innate immune system or nonspecific immunity was deployed to protect interior tissues from thermal stress. In addition, 85% of the mutual DEGs were involved in bidirectional regulation (up/down or down/up) when the oysters were removed from the thermal stress to recover. This study provides preliminary insight into the molecular response of C. sikamea (♀) and C. gigas (♂) hybrids to thermal stress and provides a basis for future studies on temperature-adaptation and the possible expansion of hybrid breeding. [ABSTRACT FROM AUTHOR]

The hybridization experiments have been made between Crassostrea ariakensis and C. gigas several times. However, it is difficult to obtain a large number of hybrid offspring, which becomes the bottleneck of subsequent cross‐breeding. To explore whether the production of hybrid larvae is affected by salinity, we investigated the effects of salinity (16, 20, 24, 28 and 32 psu) on the early activities of artificial hybridization between C. ariakensis and C. gigas at 23–24°C. In this study, the results showed that during artificial insemination, the appropriate salinity of high‐quality gametes in C. ariakensis and C. gigas was 20–32 psu and 24–32 psu respectively. Besides, the fertilization rate of AG (C. ariakensis♀ × C. gigas♂) and GA (C. gigas♀ × C. ariakensis♂) at 24–28 psu was significantly (p <.05) higher than that at 16–20 psu. For incubation, the optimal salinity of embryo incubation was 28 psu, under which all embryos of AG and GA can develop rapidly to the D‐larvae and yielded a high hatching rate. During larval rearing, the larval shell height and survival rate of AG were of no significant difference (p >.05) at all salinities, and the optimum salinity for larval growth and survival of GA was 24–28 psu. These findings can contribute to the increase in the hybrid progeny yield, which can serve as the new resource for genetic improvement of oyster germplasm. [ABSTRACT FROM AUTHOR]

The triploid technology is a new frontier in shellfish aquaculture and has shown encouraging results in numerous shellfish species. We induced triploid larvae in the Yesso scallop, Patinopecten yessoensis, using hyperosmotic shock for the first time in this study. Different induction parameters, including salinity strength, treatment starting point, and the duration, were tested. The highest triploid ratio of D‐shaped larvae (72.12%) was obtained by 60 ppt salinity treatment for 20 min at the first appearance of zygote showing polar body II (PB2). A significantly faster growth rate was observed during the swimming larvae stage despite a decrease in the hatching and survival ratios. The triploid ratio decreased to 46.67%, and approximately 1.76 million triploid juveniles were harvested after 90 days of cultivation. The treatment parameters can be further optimized to improve the yield of Yesso scallop triploids. [ABSTRACT FROM AUTHOR]

Abstract: Hybridization breeding is deemed to be an effective countermeasure in coping with the genetic decline among marine culture species. Hybrids of Crassostrea angulata ♂ × Crassostrea sikamea ♀ have been shown to express heterosis in nutritive components and tolerance to hypotonic environments. As intertidal zone organisms, they also experience fluctuations in water temperature. To better understand the cellular and molecular processes of this hybrid species under cold stress, we analyzed the transcriptional response of hybrids after 24 hr of exposure to a low temperature of 12°C. A total of 765 differentially expressed genes were obtained, 493 of which were up‐regulated and 272 were down‐regulated. Compared to the controls treated at 25°C, energy and amino acid metabolism, protein synthesis, transport and degradation of the hybrids were suppressed. Additionally multiple biochemical and physiological‐related proteins and processes were affected to help organisms survive including integrin‐linked kinase (part of the PPAR signalling pathway), phenylalanine hydroxylase, GTP binding protein, heat shock proteins and immunity related signalling pathways. Our results provide a relatively comprehensive view about cold tolerance in this oyster hybrid species, offering a more solid theoretical foundation for further study and possible expansion of hybrid cultivation. [ABSTRACT FROM AUTHOR]

Background: Recent studies have shown that XihuangWan (XHW) is a kind of Chinese medicine with significant anti-tumor and anti-inflammatory activities. However, its mechanism for preventing and treating radiation proctitis in rectal cancer patients during radiotherapy remains unclear., Methods: This study employed the network pharmacology to establish a "drug-active ingredient-target genedisease" network via using TCMSP, SymMap, GeneCard, and OMIM databases. The PPI network was conducted by the String tool. The core targets of XHW in the treatment of rectal cancer and radiation enteritis were identified by topological analysis, and the functional annotation analysis and pathway enrichment analysis were performed., Results: A total of 61 active ingredients of XHW ingredients, 4607 rectal cancer-related genes, 5803 radiation enteritis-related genes, and 68 common targets of XHW in the treatment of rectal cancer and radiation enteritis were obtained. PTGS1 and NR3C2, as identified potential targets, were significantly associated with OS of colorectal cancer patients. GO and KEGG enrichment analysis showed that bioinformatics annotation of these common genes was mainly involved in DNA-binding transcription factor, PI3K/Akt, TNF, HIF-1 signaling pathway, and colorectal cancer pathway., Conclusion: The active ingredients of XHW, mainly including Quercetin, Ellagic acid, and Stigmasterol, might act on common targets of rectal cancer and radiation enteritis, such as PTGS1, NR3C2, IL-6, EGFR, HIF-1A, CASP3, BCL2, ESR1, MYC, and PPARG, and regulate multiple signaling pathways like PI3K-Akt, TNF, and HIF-1 to inhibit tumor proliferation, tumor angiogenesis, inflammatory responses, and oxidative stress, thereby achieving prevention and treatment of radiation enteritis in rectal cancer patients during radiotherapy. It provided an important reference for further elucidating the anti-inflammation and anti-tumor mechanism and clinical application of XHW., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella , Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.