Institute of Hydrobiology, Chinese Academy Of Sciences
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Comparative exposomics of persistent organic pollutants (PCBs, OCPs, MCCPs and SCCPs) and polycyclic aromatic hydrocarbons (PAHs) in Lake Victoria (Africa) and Three Gorges Reservoir (China) (vol 695, 133789, 2019)
No full textResequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence
No full textCoffea arabica, C. canephora and C. excelsa, with differentiated morphological traits and distinct agro-climatic conditions, compose the majority of the global coffee plantation. To comprehensively understand their genetic diversity and divergence for future genetic improvement requires high-density markers. Here, we sequenced 93 accessions encompassing these three Coffea species, uncovering 15,367,960 single-nucleotide polymorphisms (SNPs). These SNPs are unequally distributed across different genomic regions and gene families, with two disease-resistant gene families showing the highest SNP density, suggesting strong balancing selection. Meanwhile, the allotetraploid C. arabica exhibits greater nucleotide diversity, followed by C. canephora and C. excelsa. Population divergence (F-ST), population stratification and phylogeny all support strong divergence among species, with C. arabica and its parental species C. canephora being closer genetically. Scanning of genomic islands with elevated F-ST and structure-disruptive SNPs contributing to species divergence revealed that most of the selected genes in each lineage are independent, with a few being selected in parallel for two or three species, such as genes in root hair cell development, flavonols accumulation and disease-resistant genes. Moreover, some of the SNPs associated with coffee lipids exhibit significantly biased allele frequency among species, being valuable for interspecific breeding. Overall, our study not only uncovers the key population genomic patterns among species but also contributes a substantial genomic resource for coffee breeding.
Key message Whole-genome resequencing of 93 coffee accessions unveils diversity and genetic relationship of three important Coffea species. Independent and parallel selection of genes are identified during the three species divergenc
Immune Responses of the Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis ssp. asiaeorientalis) to Escalating Anthropogenic Stressors in the Wild and Seminatural Environments
No full textIncreasing anthropogenic stressors are potential threats to biodiversity conservation and management of Yangtze finless porpoises (YFPs). The objective of this study was to indirectly compare the habitat quality of a natural reserve, Poyang Lake and a seminatural reserve, the Tian-E-Zhou Oxbow (TZO) in terms of anthropogenic stressors by investigating different stress and immunological parameters in the blood of YFPs. Samples from a total of 74 YFPs from the TZO (n = 43) and Poyang Lake (n = 31) were collected and analyzed. The animals were divided into ontogenetic groups: male calf, female calf, juvenile female, juvenile male, and adult male, and reproductive groups: pregnant female, lactating female, and pregnant plus lactating. The blood from all the animals was analyzed for general stress (HSP14, SOD1, TXN, and FTL), metabolic stress (ACAT2 and THRA), and immunity-related genes (IL12p40, IFN gamma, TNF alpha; IL1 alpha, IL1ra, COX2, CRPL, IL4, and IL8) using qPCR. YFPs living in Poyang Lake showed an increased relative expression pattern for IFN gamma, IL1ra, IL4, ACAT2, and CRPL across all the ontogenetic groups with significantly higher expression in adult males. In contrast, YFPs living in the TZO showed a significantly higher expression in 13 of 15 genes analyzed in the male calf group. Across the reproductive states for porpoises living in Poyang Lake, eight of the 15 genes in the pregnant female and three of the 15 genes in the pregnant plus lactating group had a significantly higher expression level. However, in YFPs living in the TZO, eight of the 15 genes showed significantly higher expression in the pregnant and lactating groups. There was significantly a higher expression of most of the genes in porpoises living in the TZO compared to the age-matched groups from porpoises living in Poyang Lake. The exception was the pregnant female group. The higher relative expression of stress and immune genes in the TZO porpoise population compared to porpoises living in Poyang Lake suggests the effects of worsening habitat quality, possibly indicating water pollution and lack of feeding resources
C, N, and P stoichiometry and their interaction with different plant communities and soils in subtropical riparian wetlands
No full textEcological stoichiometry represents the balance of nutrient elements under ecological interactions, which are crucial for biogeo-chemical cycles in ecosystems. Little is known about carbon (C), nitrogen (N), and phosphorus (P) ecological stoichiometry in aboveground biomass, roots, and soil, especially in the subtropical riparian wetlands. Here, eight dominate plant communities in riparian wetlands were chosen, and C, N, and P contents, and C:N:P ratios of aboveground biomass, roots, and soil were investigated. The results demonstrated that plant community had remarkable effects on the C:N:P stoichiometry in aboveground biomass, roots, and soil, which varied widely. C, N, and P concentrations in aboveground biomass were mostly higher than that in roots, while no significant difference was detected in C:N:P ratios. Moreover, there were higher soil C, N, and P contents in Cannabis indica plant communities; while lower soil N:P ratios suggested that riparian wetlands were more susceptible to N limitation, rather than P. Pearson correlation analysis and redundancy analysis (RDA) showed that there were strong associations among C, N, and P contents, and C:N:P ratios in aboveground biomass, roots, and soil, indicating that C, N, and P ecological stoichiometry of aboveground biomass were regulated by soil C, N, and P contents through the roots. In addition, the contents of C and N, and N and P exhibited a strong relationship according to linear regression. These findings suggested that the interactions among the C, N, and P stoichiometry were existed in the plant-soil system.</p
Assessment of Cu, Zn, Mn, and Fe enrichment in Mt. Kenya soils: evidence for atmospheric deposition and contamination
No full textMountains are the preferred sites for studying long-range atmospheric transportation and deposition of heavy metals, due to their isolation and steep temperature decrease that favors cold trapping and condensation of particulate forms of heavy metals. Any enrichment of heavy metals in mountains is presumed to primarily occur through atmospheric deposition. In this particular study, we assessed the status of 27 subsurface soils collected along two elevation gradients of Mt. Kenya using enrichment factors (EFs) as the ecological risk assessments. The collected soils were analyzed for total organic carbon, zinc (Zn), iron (Fe), manganese (Mn), and copper (Cu). The mean concentration of Mn, Fe, Zn, and Cu was 0.376 mg/kg, 47.6 mg/kg, 12.3 mg/kg, and 4.88 mg/kg in Chogoria and 0.560 mg/kg, 113 mg/kg, 12.7 mg/kg, and 2.70 mg/kg in Naro Moru respectively. These concentrations were below the US-EPA maximum permissible levels for soils, implying that the levels recorded had low toxicity. Meanwhile, the mean enrichment factors for Mn, Cu, and Zn were 0.447, 131, and 78.8 in Chogoria and 0.463, 38.9, and 53.0 in Naro Moru respectively. This implied that Zn and Cu in Chogoria sites were extremely enriched, while in Naro Moru, enrichment levels ranged from significant to extreme. However, Mn was found to have minimal enrichment in all the sites. Lower montane forest and bamboo zone recorded relatively high enrichment due to distance from source of pollution. Ericaceous zone also had high mean enrichment due to influence of wind which favors higher deposition at mid-elevations
A rapid and reliable method for identifying genetic sex in obscure pufferfish (Takifugu obscures)
No full textObscure pufferfish (Takifugu obscurus) is an important aquaculture species in China, and sex control breeding is extremely attractive in this species because the testes of male pufferfish are more popular and expensive. However, the sex-specific marker remains unknown and reliable genetic sex identification method has not been established, which has hampered the development of monosexual aquaculture. In this study, the sex-linked amhr2 SNP site of obscure pufferfish was firstly identified by sequencing and high-resolution melting (HRM) analysis. The males exhibit heterozygous genotype (C/G), while females have homozygous genotype (C/C), which is identical to its closely-related species (T. rubripes, T. poecilonotus and T. pardalis). Then, two pairs of male-specific primers were designed based on the sex-specific SNP site and a high-throughput sexing method was subsequently developed with benefits including high specificity and superb sensitivity. Particularly, this method has greatly reduced analysis time and costs compared to the previously established HRM analysis. These results will be beneficial to develop the sex control breeding in obscure pufferfish
Anti-foodborne enteritis effect of galantamine potentially via acetylcholine anti-inflammatory pathway in fish
No full textFoodbome enteritis has become a limiting factor in aquaculture. Plant protein sources have already caused enteritic inflammation and inhibition in growth performance. Attempts have been made to find an effective solution to foodbome enteritis. Based on the previously suggested fish cholinergic anti-inflammatory pathway, galantamine, a typical cholinesterase inhibitor, was tested for the repression of pro-inflammatory cytokines for soybean meal induced enteritis by injection into grass carp. Both the phylogenetic analysis of cholinesterase, AchR and bioinformatic prediction, indicated galantamine's potential use as an enteritis drug. The result highlighted galantamine's potential effect for anti-enteritis in fish, especially in carps. Subsequently, a 4-week feeding trail using galantamine as an additive, in a zebrafish soybean meal induced enteritis model, demonstrated the prevention of enteritis. The results demonstrated that galantamine could prevent intestinal pathology, both histologically and molecularly, and also maintain growth performance. Reflected by gene expressional analysis, all mechanical, chemical and immune functions of the intestinal barrier could be protected by galantamine supplementation, which aided molecularly in the control of fish foodbome enteritis, through down-regulating Th17 type proinflammatory factors, meanwhile resuming the level of Treg type anti-inflammatory factors. Therefore, the current results shed light on fish intestinal acetylcholine anti-inflammation, by the dietary addition of galantamine, which could give rise to protection from foodbome enteritis
The Reproductive Strategy of the Rare Minnow (Gobiocypris rarus) in Response to Starvation Stress
No full textFood abundance plays an important role in the reproduction of fish, especially multiple spawners. Multiple spawners can exhibit various biological strategies when under starvation stress. However, the reproductive strategy used in these fish species remains unknown. To explore whether rare minnows (Gobiocypris rarus) prioritize survival over current reproduction under starvation conditions, paired adult rare minnows were starved for 0, 5, 10, 15 d and their spawning activities were recorded. Anatomical and histological characteristics of unpaired adult rare minnows were examined during starvation and following re-feeding. It was found that only 30-70% of paired rare minnows spawned within 5 d after deprivation of food. Though spawning activity was suppressed by starvation, rare minnows starved for 0, 5, 10, and 15 d waited 3.89 +/- 0.78 d, 5.57 +/- 3.36 d, 5.83 +/- 5.15 d and 6.57 +/- 4.50 d, respectively, after re-feeding to resume spawning. The average inter-spawning interval and length until egg production of those starved for 15 d was 4.60 +/- 2.37 d and 139.1 +/- 67.9 d, respectively, when they spawned with rhythm, which were significantly different from those starved for 0 d (P < 0.05). Anatomical and histological data further revealed that late maturing oocytes degraded after 8 d of starvation, but the gonadosomatic index recovered to initial levels after 8 d of re-feeding. Thus, reproduction of rare minnows was markedly affected by starvation, but rapidly returned to normal upon re-feeding. These observations demonstrated that paired rare minnows prioritize survival by channeling energy from the liver and absorbing late maturing oocytes instead of continuing to reproduce under food deprivation condition
Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts
No full textThe majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it
Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts
No full textThe majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.</p