Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis)

Chinese tongue sole is a marine fish with ZW sex determination. Genome sequencing suggested that the Z-linked dmrt1 is a putative male determination gene, but direct genetic evidence is still lacking. Here we show that TALEN of dmrt1 efficiently induced mutations of this gene. The ZZ dmrt1 mutant fish developed ovary-like testis, and the spermatogenesis was disrupted. The female-related genes foxl2 and cyp19a1a were significantly increased in the gonad of the ZZ dmrt1 mutant. Conversely, the male-related genes Sox9a and Amh were significantly decreased. The dmrt1 deficient ZZ fish grew much faster than ZZ male control. Notably, we obtained an intersex ZW fish with a testis on one side and an ovary on the other side. This fish was chimeric for a dmrt1 mutation in the ovary, and wild-type dmrt1 in the testis. Our data provide the first functional evidence that dmrt1 is a male determining gene in tongue sole

The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation(1-5). The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways. We demonstrate that retinoic acid is critical in establishing asymmetric pigmentation and, via cross-talk with thyroid hormones, in modulating eye migration. The unexpected expression of the visual opsins from the phototransduction pathway in the skin translates illumination differences and generates retinoic acid gradients that underlie the generation of asymmetry. Identifying the genetic underpinning of this unique developmental process answers long-standing questions about the evolutionary origin of asymmetry, but it also provides insight into the mechanisms that control body shape in vertebrates.National Natural Science Foundation of China [31130057, 31461163005, 31530078, 31472269, 31472262, 31472273]; State 863 High Technology R&D Project of China [2012AA092203, 2012AA10A408, 2012AA10A403-2]; Education and Research of Guangdong Province [2013B090800017]; Taishan Scholar Climb Project Fund of Shandong of China; Taishan Scholar Project Fund of Shandong of China for Young Scientists; Shanghai Universities First-class Disciplines Project of Fisheries; Program for Professor of Special Appointment (Eastern Scholar) at the Shanghai Institutions of Higher Learning; Shanghai Municipal Science, Special Project on the Integration of Industryinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/publishedVersio

The chromosomal-level genome of <i>Oryzias sinensis reveals</i> chromosome fusion among ricefish.

The chromosome assembly file of Oryzias sinensis</p

Weighted Gene Co-Expression Network Analysis of red body color formation of crimson snapper, Lutjanus erythropterus

Crimson snapper (Lutjanus erythropterus) is a highly valued economic fish species, with its red body color being a crucial economic characteristic. A systematic study of skin pigmentation could offer insights into the mechanism of red coloration. In this study, we conducted the first network analysis of snapper transcriptomes during key developmental stages of pigmentation, identifying a cascade of cellular development and responsive gene modules and key genes, including eight developmental-specific modules. Among the four candidate hub genes (TNNT2, ROBO2, APBA2, and APOD), APOD was involved in pigmentation development. The network further revealed some key genes, such as TYRP1a, TYRP1b, PMEL, BCO1, BCO2, CYP2J2, CYP2J6, CYP3A4, PNPLA2, FABP6, ENPP7, and FFAR3, associated with melanin synthesis, carotenoids, and lipid metabolism. Our findings showed that pteridine and carotenoids were involved in yellow coloration after initial feeding, while yellow pigmentation-related genes (e.g., GCH1, PTS, SPR, CBR1, SCARB1, CD36, ABCA1, NpC1L1, etc.) had the same expression pattern at three days post-hatching (3 dph). At the red coloration emergence stage (45 dph), we observed an RNA level signal indicating the conversion of coloring substances from pteridine to carotenoids. These results substantially enhance understanding of the molecular mechanisms underlying pigmentation and skin color variation in L. erythropterus, providing a theoretical basis for improving of body coloration in economically cultured fish and genetic breeding of ornamental fish

A Potential Role of the Translation Elongation Factor eef1a1 in Gonadal High-Temperature Perception in Chinese Tongue Sole (Cynoglossus semilaevis)

The eukaryotic translation elongation factor 1 alpha (eef1a) gene has a well-defined role in protein synthesis. However, its role in external temperature perception and internal sex differentiation and development is still unclear. In this study, eef1a1 was identified and functionally analyzed in Chinese tongue sole (Cynoglossus semilaevis). The eef1a1 cDNA, 1809 bp in length, had a 1386 bp open reading frame (ORF) that encoded a 461 amino acid polypeptide containing one EF-1_alpha domain. eef1a1 expression levels were investigated across different tissues and during gonadal development. In the gonad, eef1a1 showed a sexually dimorphic expression pattern with a statistically higher expression level in the ovary than in the testis from 6 months postfertilization to 3 years postfertilization. Under high temperature (28 &deg;C) treatment during C. semilaevis sex differentiation (from 30 days postfertilization to 3 months postfertilization), eef1a1 was statistically down-regulated in males, while the difference was not detected in females. In addition, the dual-luciferase assay exhibited that eef1a1 can respond to high temperature rapidly. Based on these results, C. semilaevis eef1a1 might have a dual role in the perception of external temperature changes and sex differentiation regulation

Oryzias curvinotus in Sanya Does Not Contain the Male Sex-Determining Gene dmy

Hainan medaka (Oryzias curvinotus) is distributed in the coastal waters of the South China Sea and is able to adapt to a wide range of salinities. In this study, we characterized O. curvinotus in Sanya River (SY-medaka), which lacks dmy (a male sex-determining gene in O. latipes and O. curvinotus). In a comparison of SY-medaka and Gaoqiao medaka (GQ-medaka), the morphological difference between the two populations does not reach the subspecies level and they can be considered two geographic populations of O. curvinotus. A mitochondrial cytochrome oxidase subunit I (CoI) sequence alignment showed that the sequence identities between SY-medaka and other geographic populations of O. curvinotus are as high as 95%. A phylogenetic analysis of the mitochondrial genome also indicated that SY-medaka belongs to O. curvinotus. Molecular marker-based genetic sex assays and whole genome re-sequencing showed that SY-medaka does not contain dmy. Further, in RNA-Seq analyses of the testis and ovaries of sexually mature SY-medaka, dmy expression was not detected. We speculate that high temperatures resulted in the loss of dmy in SY-medaka during evolution, or the lineage has another sex-determining gene. This study provides a valuable dataset for elucidating the mechanism underlying sex determination in Oryzias genus and advances research on functional genomics or reproduction biology in O. curvinotus

The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data

Abstract Eretmochelys imbricata, a critically endangered sea turtle inhabiting tropical oceans and protected across the world, had an unknown genome sequence until now. In this study, we used HiFi reads and Hi-C technology to assemble a high-quality, chromosome-level genome of E. imbricata. The genome size was 2,138.26 Mb, with contig N50 length of 123.49 Mb and scaffold N50 of 137.21 Mb. Approximately 97.52% of the genome sequence was anchored to 28 chromosomes. A total of 20,206 protein-coding genes were predicted. We also analyzed the evolutionary relationships, gene family expansions, and positive selection of E. imbricata. Our results revealed that E. imbricata diverged from Chelonia mydas 38 million years ago and had enriched olfactory receptors and aging-related genes. Our genome will be useful for studying E. imbricata and its conservation

Life Cycle Environmental Impact Assessment of Circular Agriculture: A Case Study in Fuqing, China

The process for reasonably evaluating the potential impacts of circular agriculture on the environment has become a key issue in the sustainable development of circular agriculture. Based on this consideration, by using Life Cycle Assessment (LCA) and focusing on the circular agriculture industry company of Xingyuan, Fuqing, this paper evaluates the potential impacts of the pig farming industry-dragon fruit planting-forage planting-fishery industry-mushroom planting-biogas generating-organic fertilizer production circular agriculture model compared to a main agriculture industrial model, the pig farming industry, from environmental and environmental-economic perspectives. Moreover, this paper determines key elements that restrict the development of circular agriculture through a sensitivity analysis. The results show that if we simply consider the potential environmental impacts, circular agriculture does not produce better results than those of the main agricultural production model. In addition, if we consider reducing the potential environmental impact as well as improving the economic benefits from the perspective of a &ldquo;reduction ring&rdquo;, we should consider removing mushroom planting and organic fertilizer from the circular agriculture framework. Moreover, if we want to reduce the potential environmental impact without changing the current recycling model, we should focus on the premix components, especially the three main components of corn, soybean meal, and whey protein concentrate

Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago (<i>Sillago sihama</i>)

Silver sillago (Sillago sihama) is an emerging commercial marine aquaculture species in China. To date, fundamental information on S. sihama, such as genomic information, is lacking, and no data are available on the gonad transcriptome of S. sihama. Here, the first gonadal transcriptomes of S. sihama have been constructed and genes potentially involved in gonadal development and reproduction identified. Illumina sequencing generated 60.18 million clean reads for the testis and 59.10 million for the ovary. All reads were assembled into 74,038 unigenes with a mean length of 1,004 bp and N50 value of 2,190 bp. Among all the predictable unigenes, a total of 34,104 unigenes (46%) were searched against multiple databases, including 33,244 unigenes annotated in the RefSeq Non- Redundant database at NCBI, and 28,924 in Swiss-Prot. By comparing the ovary and testis, 35,367 unigenes were identified as being differentially expressed between males and females, of which 29,127 were upregulated in the testis and 6,240 were upregulated in the ovary. Numerous differentially expressed genes (DEGs) known to be involved in gonadal development and gametogenesis were identified, including amh, dmrt1, gsdf, cyp19a1a, gnrhr, and zps. Using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, the top 20 KEGG pathways with highest number of DEGs were found to be involved in regulating gonadal development and gametogenesis in S. sihama. Moreover, 22,666 simple sequence repeats (SSRs) were identified in 14,577 SSR-containing sequences. The findings provide a valuable dataset for future functional analyses of sex-associated genes and molecular marker assisted selection in S. sihama.</i