Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus

Analysis of Pickled Cucumber Products, Based on Microbial Diversity and Flavor Substance Detection

Changes to the microbial community during pickled cucumber fermentation were studied using the 16S rDNA technique. The changes of volatile organic compounds (VOCs) during pickled cucumber fermentation were studied by gas chromatograph-ion mobility spectrometry. At the phylum level, Cyanophyta and Proteobacteria were the dominant flora in the natural fermentation group, and Firmicutes were the dominant flora in the added-bacteria fermentation group. At the generic level, the addition of Lactobacillus led to changes in the community of the bacteria in the added-bacterial fermentation group and decreased the species abundance of other bacteria. In total, 75 volatile organic compounds were identified from naturally fermented pickled cucumber, and 60 volatile organic compounds were identified from fermented pickled cucumber with bacterial addition. The main metabolites were esters, aldehydes, acids, alcohols, ketones, alkanes, nitriles, and alkenes. These metabolites will bring their unique aroma components to the pickled cucumber. Metabolomic analysis of the O2PLS model showed that Weissella and Lactobacillus were closely and positively correlated with nine alcohols, six esters, five aldehydes, four acids, three ketones, and one pyrazine. Pseudomonas and norank_f_Mitochondria show a close positive correlation with four kinds of alcohols, two kinds of esters, one kind of aldehyde, and one kind of nitrile.

Sea cucumbers: an emerging system in evo-devo

A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.

Transcriptome and co-expression network analysis reveals the molecular mechanism of inosine monophosphate-specific deposition in chicken muscle

The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.

The pentameric hydrocoel lobes organize adult pentameral structures in a sea cucumber, Apostichopus japonicus

Despite being one of the bilaterians, the body plan of echinoderms shifts from bilateral symmetry to five-fold radial, or pentaradial symmetry during embryogenesis or their metamorphosis. While the clarification of the developmental mechanism behind this transition will be a basis for understanding their unique body plan evolution, it is still poorly understood. With this regard, the hydrocoel, a mesodermal coelom formed on the left side of bilateral larva, would be a clue for understanding the mechanism as it is the first pentaradial structure that appears before metamorphosis and develops into the water vascular system of adults. By analyzing the development of a sea cucumber, Apostichopus japonicus, we found that the hydrocoel expresses genes related in muscle and neural formation such as myosin heavy chain, tropomyosin, soxC, and elav, implying that cells of the hydrocoel contributes to muscle and neural structures in the adult. Furthermore, ablation of one of the hydrocoel lobes led to incomplete development of adult pentaradial structures. The ablation of primary hydrocoel lobes resulted in the reduction in tentacles and the ablation of secondary hydrocoel lobes resulted in the reduction in water vascular canals and nerve cords. Our findings suggest that the hydrocoel lobes may serve as a potential organizing center for establishing the pentaradial body plan in echinoderms.

Differential regulation of intramuscular fat and abdominal fat deposition in chickens

Background

Chicken intramuscular fat (IMF) content is closely related to meat quality and performance, such as tenderness and flavor. Abdominal fat (AF) in chickens is one of the main waste products at slaughter. Excessive AF reduces feed efficiency and carcass quality.

Results

To analyze the differential deposition of IMF and AF in chickens, gene expression profiles in the breast muscle (BM) and AF tissues of 18 animals were analyzed by differential expression analysis and weighted co-expression network analysis. The results showed that IMF deposition in BM was associated with pyruvate and citric acid metabolism through GAPDH, LDHA, GPX1, GBE1, and other genes. In contrast, AF deposition was related to acetyl CoA and glycerol metabolism through FABP1, ELOVL6, SCD, ADIPOQ, and other genes. Carbohydrate metabolism plays an essential role in IMF deposition, and fatty acid and glycerol metabolism regulate AF deposition.

Conclusion

This study elucidated the molecular mechanism governing IMF and AF deposition through crucial genes and signaling pathways and provided a theoretical basis for producing high-quality broilers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08538-0.

Distinguishing Evolutionary Conservation from Derivedness

While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Simple Summary

Slow growth and germplasm degradation have restricted the sustainable commercial development of the sea cucumber industry. To analyze the genetic mechanism of growth traits of sea cucumbers, we constructed a high-density genetic linkage map based on single nucleotide polymorphism (SNP) molecular markers and performed a quantitative trait loci (QTL) mapping analysis. We annotated a critical candidate gene related to growth traits and explored mRNA expression levels. The results showed that the gene was significantly highly expressed during the larval developmental stages. These results can be used to genetically improve the growth traits of sea cucumbers.

Abstract

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms

Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named "derivedness index" to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.

Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya.

Li et al. investigate the evolution and genetic basis of the adult pentameral body plan in echinoderms using genomic, transcriptomic, and proteomic data. They determine that the last common ancestor of echinoderms contained an organized Hox cluster and endoskeleton genes, and suggest that cooption of bilateral development genes was involved in evolution of the pentameric body plan.

Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

Background

The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq.

Results

Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (10⁷ cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R² = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h.

Conclusion

A de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) and V. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.

The role of the hyaline spheres in sea cucumber metamorphosis: lipid storage via transport cells in the blastocoel

Background

For echinoderms with feeding larvae, metamorphic and post-settlement success may be highly dependent on larval nutrition and the accumulation of energetic lipids from the diet. In contrast to the sea urchins, starfish and brittle stars within the Phylum Echinodermata, sea cucumber metamorphosis does not involve formation of a juvenile rudiment, but instead there is a rearrangement of the entire larval body. Successful metamorphosis in sea cucumbers is often associated with the presence in the late auricularia stage of an evolutionary novelty, the hyaline spheres (HS), which form in the base of the larval arms. Known since the 1850s the function of these HS has remained enigmatic—suggestions include assistance with flotation, as an organizer for ciliary band formation during metamorphosis and as a nutrient store for metamorphosis.

Results

Here using multiple methodologies (lipid mapping, resin-section light microscopy, lipid and fatty acid analyses) we show definitively that the HS are used to store neutral lipids that fuel the process of metamorphosis in Australostichopus mollis. Neutral lipids derived from the phytoplankton diet are transported by secondary mesenchyme cells (“lipid transporting cells”, LTC), likely as free fatty acids or lipoproteins, from the walls of the stomach and intestine through the blastocoel to the HS; here, they are converted to triacylglycerol with a higher saturated fatty acid content. During metamorphosis the HS decreased in size as the triacylglycerol was consumed and LTC again transported neutral lipids within the blastocoel.

Conclusion

The HS in A. mollis functions as a nutrient storage structure that separates lipid stores from the major morphogenic events that occur during the metamorphic transition from auricularia–doliolaria–pentactula (settled juvenile). The discovery of LTC within the blastocoel of sea cucumbers has implications for other invertebrate larvae with a gel-filled blastocoel and for our understanding of lipid use during metamorphosis in marine invertebrates.

Weighted gene coexpression network analysis identifies specific transcriptional modules and hub genes related to intramuscular fat traits in chicken breast muscle

Intramuscular fat (IMF) traits are important factors that influence meat quality. However, the molecular regulatory mechanisms that underlie this trait in chickens are still poorly understood at the gene coexpression level. Here, we performed a weighted gene coexpression network analysis between IMF traits and transcriptome profile in breast muscle in the Chinese domestic Gushi chicken breed at 6, 14, 22, and 30 weeks. A total of 26 coexpressed gene modules were identified. Six modules, which included the dark gray, purple, cyan, pink, light cyan, and blue modules, showed a significant positive correlation (P < 0.05) with IMF traits. The strongest correlation was observed between the dark gray module and IMF content (r = 0.85; P = 4e-04) and between the blue module and different fatty acid content (r = 0.87~0.91; P = 5e-05~2e-04). Enrichment analysis showed that the enrichment of biological processes, such as fatty acid metabolic process, fat cell differentiation, acylglycerol metabolic process, and glycerolipid metabolism were significantly different in the six modules. In addition, the 32, 24, 4, 7, 6, and 25 hub genes were identified from the blue, pink, light cyan, cyan, dark gray, and purple modules, respectively. These hub genes are involved in multiple links to fatty acid metabolism, phospholipid metabolism, cholesterol metabolism, diverse cellular behaviors, and cell events. These results provide novel insights into the molecular regulatory mechanisms for IMF-related traits in chicken and may also help to uncover the formation mechanism for excellent meat quality traits in local breeds of Chinese chicken.

Reference assembly and gene expression analysis of Apostichopus japonicus larval development

The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages-blastula, gastrula, auricularia, pentactula-on an Illumina sequencer. Based on our RNA-seq data and the paired-end reads from 16 libraries obtained by other researchers earlier, we have achieved the currently most complete transcriptome assembly for A. japonicus with the best basic statistical parameters. An analysis of the obtained transcriptome has revealed 174 differentially expressed transcription factors, as well as stage-specific transcription factors that are most promising for further study. In addition, a total of 1,174,999 high-quality single nucleotide polymorphisms have been identified, including 58,932 indels. A GO enrichment analysis of contigs containing polymorphic loci shows the predominance of GO terms associated with immune response. The data obtained by us provide an additional basis for a deeper study of the mechanisms of the planktotrophic-type development in holothurians and can be used in commercial sea cucumber breeding programs.

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice

Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.