A chromosome-level genome assembly of the Echiura Urechis unicinctus.

Echiura is a distinctive family of unsegmented sausage-shaped marine worms whose phylogenetic relationship still needs strong evidence from the phylogenomic analysis. In this family, Urechis unicinctus is known for its high nutritional and medicinal value and adaptation to harsh intertidal conditions. Herein, we combined PacBio long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of U. unicinctus. The assembled genome spans ~1,138.6 Mb with a scaffold N50 of 68.3 Mb, of which 1,113.8 Mb (97.82%) were anchored into 17 pseudo-chromosomes. The BUSCO analysis demonstrated the completeness of the genome assembly and gene model prediction are 93.5% and 91.5%, respectively. A total of 482.1 Mb repetitive sequences, 21,524 protein-coding genes, 1,535 miRNAs, 3,431 tRNAs, 124 rRNAs, and 348 snRNAs were annotated. This study significantly improves the quality of U. unicinctus genome assembly, sets the footsteps for molecular breeding and further study in genome evolution, genetic and molecular biology of U. unicinctus.

Identification and expression analysis of Oxfibrillin gene involved in the regeneration process of Ophryotrocha xiamen (Annelida, Dorcilleidae).

Regeneration of lost body parts is a widespread phenomenon across annelids. However, the molecular inducers of the cell sources for this reparative morphogenesis have not been identified. We have identified a regeneration-related gene Oxfibrillin from the transcriptome analysis of a polychaeta, Ophryotrocha xiamen, which is found to be a well-suited model to study the mechanisms of regeneration. Fibrillins are large glycoproteins that assemble to form the microfibrils and regulate growth factors or other transfer processes. Here, we obtained the 31,274 bp genomic DNA sequences of Oxfibrillin. The coding sequence length was 5784 bp encoding 1927 amino acids with a VWD domain, EGF/cb-EGF domains, a TR domain, and a transmembrane domain. Oxfibrillin was positioned within the subgroup of invertebrates and showed low scores for homology to mammalian fibrillin. In gene expression analysis, Oxfibrillin genes were constantly upregulated during the early regeneration process and then remained stable until the formation of the complete tail which indicated that it might be a vital factor to affect posterior regeneration process. Therefore, the Oxfibrillin of O. xiamen might play important roles in the regeneration process.

The preparation of hybrid silicon quantum dots by one-step synthesis for tetracycline detection and antibacterial applications.

In this study, we prepared three different silicon quantum dots (SiQDs-1, SiQDs-2 and SiQDs-3) by hydrothermal synthesis with rose Bengal as the reducing agent and triacetoxy(methyl)silane and allyloxytrimethylsilane as silicon sources. The as-prepared SiQDs not only exhibited potent antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) but also showed specific responses to tetracycline (TC). The minimum inhibitory concentrations (MICs) of SiQDs-1, SiQDs-2 and SiQDs-3 were 0.55 mg mL-1, 0.47 mg mL-1 and 0.39 mg mL-1 against E. coli, respectively, and 0.45 mg mL-1, 0.34 mg mL-1 and 0.34 mg mL-1 against S. aureus, respectively. By examining the morphologies of bacteria and generation of reactive oxygen species (ROS), we speculated that these SiQDs shrink the bacteria and even directly destroy the bacterial structural integrity through the production of singlet oxygen. In addition, the fluorescence quenching effectiveness of SiQDs-3 also showed a strong linear relationship with TC concentration in the range of 0-1.2 µM with a detection limit of 0.318 µM, as a result of the internal filtering effect. Together, SiQDs not only can be a candidate to treat resistant bacterial infections, but also may be applied in practical detection of TC.

First report of powdery mildew on Astragalus sinicus (Chinese milk vetch) caused by Erysiphe trifoliorum in China.

Astragalus sinicus L., (Chinese milk vetch) is a traditional leguminous green manure that plays a significant role in maintaining paddy soil fertility to enhance yield and the quality of rice in China. It is also found in gardens, roadsides, farms, fields, riverbanks, open wastelands, and is often used as livestock feed. From February 2019 to 2021, severe powdery mildew infections were observed on hundreds of A. sinicus grown in gardens and at roadsides of Fuzhou city, China. The disease incidence was up to 100% on leaves and stems of A. sinicus. White superficial fungal colonies (circular to irregular patches) were present on both sides of the leaves. Hyphae were flexuous to straight, branched, 4 to 8 µm in width, and septate. Hyphal appressoria were lobulate and solitary or in opposite pairs. Conidiophores were erect and straight, hyaline, and 60 to 120 × 8 to 10 µm (n=30). Foot cell was cylindrical, straight to slightly curved, 22 to 38 × 8 to 10 µm, followed by two to three shorter cells. Conidia were cylindrical-oval to doliiform, 30 to 48 × 13.5 to 24 µm with a length/width ratio of 1.6 to 2.4 (n = 30), formed singly, and without fibrosin bodies. Conidial germ tubes were produced subterminal position. No chasmothecia were found in the collected samples. The morphological characteristics of asexual structures were consistent with the descriptions of E. trifoliorum (Wallr.) U. Braun in Braun and Cook (2012). To verify the identification of the pathogen, the ITS and the part of large subunit (LSU) rDNA gene of the isolates were amplified using ITS1/ITS4 and LSU1/ LSU2 primers (Scholin et al. 1994 and White et al. 1990, respectively) and sequences were deposited in GenBank (ITS: MZ021332, MZ021333; LSU: MZ021334, MZ021335). In BLASTn searches, the ITS and LSU sequences were 99 to 100% identical with those of E. trifoliorum parasitic on Lathyrus magellanicus (LC010015), Medicago littoralis (LC270860), Melilotus officinalis (LC009924) and Trifolium spp., (MN216308, KY660821), as well as E. baeumleri (Bradshaw et al. 2021) on Vicia nigricans (LC010014). Pathogenicity test was performed by gently pressing a diseased leaf onto 10 young leaves of three healthy potted plants, while three non-inoculated plants were used as controls. All plants were maintained in a greenhouse at 20 to 25°C, without humidity control, and natural light. Symptoms developed 7 days after inoculation, whereas the control leaves remained symptomless. The morphology of the fungus on the inoculated leaves was identical to that observed on the originally diseased leaves. Powdery mildew on A. sinicus has been reported as E. pisi and E. polygoni from Korea and China (Shin, 2000; Tai 1979), respectively. Amano (1986) listed E. pisi and Microsphaera astragali (now E. astragali) on A. sinicus from China and Japan. To our knowledge, this is the first report of powdery mildew caused by E. trifoliorum on A. sinicus in China and in general. E. astragali is the most common and widespread powdery mildew species on Astragalus spp. (Braun and Cook 2012) and would be expected on A. sinicus, but this species is genetically clearly different from E. trifoliorum (Bradshaw et al. 2021). The E. trifoliorum complex (clade) is composed of several morphologically well-distinguishable species, besides E. trifoliorum also including E. baeumleri (on Vicia spp.), E. hyperici (on Hypericum spp.), and E. euonymi (on Euonymus spp.), but based on a combination of sequence plus host identity, the collection on A. sinicus can be assigned to E. trifoliorum (Bradshaw et al. 2021). The information in this study extended the host range of E. trifoliorum as well as future studies on A. sinicus in relation to powdery mildew outbreaks in China. References: Amano (Hirata), K. 1986. Host Range and Geographical Distribution of the Powdery Mildew Fungi. Japan Scientific Societies Press, Tokyo, 741 pp. Bradshaw, M., et al. 2021. Mycologia. (In press) Braun, U., Cook, R. T. A. 2012. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, the Netherlands. Scholin, C. A., et al. 1994. J. Phycol. 30:999. Shin, H.D. 2000. Erysiphaceae of Korea. National Institute of Agricultural Science and Technology, Suwon, Korea, 320 pp. Tai, F.L. 1979. Sylloge Fungorum Sinicorum. Sci. Press, Acad. Sin., Peking, 1527 pp. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA.

First Report of Powdery Mildew Caused by Podosphaera xanthii on Sigesbeckia orientalis in China.

Sigesbeckia orientalis L., (St Paul's wort) is an annually grown natural herb of Asteraceae with a long therapeutic history for a wide range of inflammation-related diseases in China (Zhong et al. 2019). In June 2020, typical symptoms of powdery mildew were observed on 30% of wild S. orientalis plants grown along the roadsides and gardens in Minjiang University, Fuzhou, China. Circular to irregular white powdery fungal colonies were observed on both surfaces of the leaves and young stems, causing necrosis and premature senescence. Fungal hyphae were epigenous, flexuous to straight, branched, and septate. Appressoria on the hyphae were nipple-shaped or nearly absent. Conidiophores were straight, 30 to 210× 8 to 12 µm, and produced 3 to 7 immature conidia in chains with a crenate outline. Foot-cells were cylindrical, 45 to 75 ×10 to 12 µm, followed by 1 to 2 shorter cells. Conidia were hyaline, ellipsoid-ovoid to barrel-shaped, 25 to 38 × 18 to 23 µm with distinct fibrosin bodies. Germ tubes were produced from a lateral position on the conidia. Chasmothecia were not observed on the infected leaves. Based on anamorph characteristics, fungus was identified as Podosphaera xanthii (Castagne) U. Braun & N. Shishkoff (Braun and Cook 2012). For molecular identification, total genomic DNA was extracted (Mukhtar et al. 2018) from fungal colonies on infected leaves of five collections separately. For each DNA sample, the part of LSU and ITS regions were amplified using primers LSU1/LSU2 and ITS1/ITS4 (Scholin et al. 1994; White et al. 1990), respectively. A BLAST search revealed 100 % sequences similarity with P. xanthii sequences reported on Ageratum conyzoides (KY274485), Eclipta prostrata (MT260063), Euphorbia hirta (KY388505), Sonchus asper (MN134013), and Verbena bonariensis (AB462804). Representative sequences (ITS: MZ613309; LSU: MZ614707) of an isolate were deposited in GenBank. The phylogenetic analysis also grouped the obtain sequences into P. xanthii clade. Pathogenicity was confirmed by gently pressing the infected leaves onto young leaves of five healthy one-month-old S. orientalis plants, while three non-inoculated plants were used as controls. All plants were maintained in a greenhouse at 25 ± 2°C. After, seven days, white powdery colonies were observed on inoculated plants, whereas controls remained mildew-free. On inoculated leaves, the fungus was morphologically and molecularly identical to the fungus on the original specimens. P. xanthii has been reported as a significant damaging pathogen on a wide range of plants in China (Farr and Rossman 2021). To our knowledge, this is the first report of powdery mildew caused by P. xanthii on S. orientalis in China as well as worldwide. S. orientalis is one of the most important commercial Chinese medicinal herbs and the occurrence of powdery mildew is a threat to its production, quality, and marketability. References: Braun, U., and Cook, R. T. A. 2012. The Taxonomic Manual of the Erysiphales (Powdery Mildews). CBS Biodiversity Series 11: CBS. Utrecht, The Netherlands. Farr, D. F., and Rossman, A. Y. 2021. Fungal Databases. Syst. Mycol. Microbiol. Lab., USDA ARS, 9 October 2021. Mukhtar, I., et al. 2018. Sydowia.70:155. Scholin, C. A., et al. 1994. J. Phycol. 30:999. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. Zhong, Z., et al., 2019. Chin. Med. (U. K.) 14, 1-12. 10.1186/s13020-019-0260-y.

First Report of Powdery Mildew Caused by Golovinomyces ambrosiae on Bidens pilosa in China.

Bidens pilosa L., (spanish needle), is a wild, flowering plant of Asteraceae, that is grown in gardens, fields, roadsides, and riverbanks in Fuzhou, China. It is also used in traditional folk medicine for a broad range of ailments in China. In March 2019 and 2020, hundreds of B. pilosa growing along the roadsides, and gardens in the districts of Minhou and Jinshan were observed to be severely affected by a powdery mildew with approximately 80% disease incidence. Symptoms appeared as circular to irregular small white, powdery patches, typically on the adaxial sides of leaves and progressed to coalescent colonies on the leaves. As the disease developed, the infected leaves became wilted and senesced. Mycelia on leaves were superficial and solitary appressoria were slightly to distinctly nipple-shaped. Conidiophores were erect, 120 to 230 × 10 to 12 µm, and produced two to five conidia in chains with a sinuate outline. Foot-cells were erect, cylindrical, and 60 to 110 µm long. Conidia were hyaline, ellipsoid to barrel-shaped, 26 to 40 × 18 to 24 µm, and devoid of distinct fibrosin bodies. Germ tubes were long and produced at the perihilar position of the conidia. No chasmothecia were observed. Morphological characteristics overlapped with Golovinomyces ambrosiae, G. cichoracearum, and G. spadiceus (Braun and Cook 2012) on hosts within the Asteraceae tribe Heliantheae (Takamatsu et al. 2013). For molecular identification, ITS and IGS regions as well as partial LSU of two representative collections (MJU-IM019- MJU-IM020), were amplified using ITS1/ITS4, IGS-12a/ NS1R and LSU1/LSU2 primers (Carbone & Kohn, 1999; Scholin et al. 1994; White et al. 1990), respectively. The resulting sequences were deposited in GenBank (ITS: MW965777, MW965778; LSU: MW965787, MW965788; IGS: MW981256, MW981257). A BLAST search revealed 99 to 100 % sequence similarity to G. ambrosiae sequences (KX987303, AB769421, AB077689, AB769426, AB077643, and AB769425). Phylogenetic analysis of ITS, LSU and IGS also grouped obtained sequences within the G. ambrosiae complex (Qiu et al. 2020). Pathogenicity was confirmed through inoculation by gently pressing infected leaves onto leaves of five healthy, potted, young B. pilosa plants, while five non-inoculated plants served as controls. All plants were maintained in a greenhouse at 25 ± 2°C. Inoculated plants developed symptoms after 7 to 10 days, whereas the control plants remained symptomless. The morphology of the resulting fungus on inoculated plants was identical to that originally observed on diseased plants. Podosphaera spp., have been reported on B. pilosa (Farr & Rossman 2021) from North America, Africa, and Asia. To our knowledge, this is the first report of powdery mildew caused by G. ambrosiae on B. pilosa in China and Asia. Wild populations of B. pilosa may be the primary source of powdery mildew inoculum for commercial Asteraceae members and may warrant consideration in the control of this disease. References: Braun, U., and Cook, R. T. A. 2012. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, The Netherlands. Carbone, I., and Kohn, L. M. 1999. Mycologia 91:553. Farr, D. F., and Rossman, A. Y. 2021. Fungal Databases. Syst. Mycol. Microbiol. Lab., USDA ARS, 18 April 2021. Qiu, P. L., et al. 2020. BMC Microbiol. 20:1. Scholin, C. A., et al. 1994. J. Phycol. 30:999. Takamatsu, S., et al. 2013. Mycologia 105:1135. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA.

First Report of Powdery Mildew Caused by Podosphaera xanthii on Cuphea hyssopifolia (Lythraceae) in Mainland China.

Cuphea hyssopifolia (Mexican heather) is a popular evergreen perennial shrub used for ornamental and medicinal purposes. Due to its high ornamental value, it is often used as a ground cover in parks and gardens in China. During February and March 2019 & 2020, powdery mildew was observed on C. hyssopifolia in the districts of Minhou and Jinshan of Fuzhou, China. Disease incidence was 70% but of low severity with only a few older leaves showing yellowing and wilting. Sparse irregular patches of white superficial powdery mildew observed on both sides of mature and young leaves. The powdery mildew fungal appressoria that occurred on epigenous hyphae, were indistinct to nipple-shaped, hyaline, and smooth. Conidiophores were erect, smooth, 80 to 210 × 10 to 12 µm, and produced two to eight crenate-shaped conidia in chains. Foot-cells of conidiophores were straight, cylindric, and 30 to 65 × 10 to12 µm. Conidia were hyaline, smooth, ellipsoid-ovoid to barrel-shaped, 25 to 38 × 16 to 20 µm with distinct fibrosin bodies. Germ tubes were simple to forked and produced from the lateral position of the germinating conidia. No chasmothecia were observed on the surface of infected leaves. Based on the morphology of the imperfect state, the powdery mildew fungus was identified as Podosphaera xanthii (Castagne) U. Braun & N. Shishkoff (Braun and Cook 2012). To confirm fungal identification, total DNA was extracted (Mukhtar et al., 2018) directly from epiphytic mycelia on infected leaves collected from both districts. Internal transcribed spacer (ITS) regions and the partial large subunit (LSU) rDNA were amplified using primers ITS1/ITS4 and LSU1/LSU2 (Scholin et al. 1994, White et al. 1990), respectively. The sequences were deposited in GenBank (ITS: MW692364, MW692365; LSU: MW699924, MW699925). The ITS and LSU sequences were 99 to 100 % identical to those of P. xanthii in GenBank, (ITS: MT568609, MT472035, MT250855, and AB462800; LSU: AB936276, JX896687, AB936277, and AB936274). Koch's postulates were completed by gently pressing diseased leaves onto leaves of five healthy potted C. hyssopifolia plants that were held in a greenhouse at 24 to 30°C without humidity control. Five non-inoculated plants served as controls. Inoculated plants developed symptoms after 6 to 10 days, whereas the controls remained symptomless. The morphology of the fungus on the inoculated leaves was identical to that observed on the originally diseased leaves. Previously, Podosphaera sp. has been reported on C. rosea in the United Kingdom (Beales & Cook 2008) and P. xanthii on C. hyssopifolia in Taiwan (Yeh et al. 2021). To our knowledge, this is the first report of powdery mildew caused by P. xanthii on C. hyssopifolia in mainland China. Our field observations suggest that the P. xanthii infections would be a potential threat to the health of C. hyssopifolia in China. References: Beales, P. A., and Cook, R. T. A. 2008. Plant Pathol. 57:778. Braun, U., Cook, R. T. A. 2012. The Taxonomic Manual of the Erysiphales (Powdery Mildews). CBS Biodiversity Series 11: CBS. Utrecht, The Netherlands. Mukhtar, I., et al. 2018. Sydowia.70:155. Scholin, C. A., et al. 1994. J. Phycol. 30:999. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. Yeh, Y. W., et al. 2021. Trop. Plant Pathol. 46:44.

Transcriptome Profiling Revealed Multiple rquA Genes in the Species of Spirostomum (Protozoa: Ciliophora: Heterotrichea).

Adaptation to life at different oxygen tensions plays a role in protozoan ecology and controls the distribution of different species in anoxic habitats. The ciliate genus Spirostomum inhabiting fresh or low salinity water globally where these species are considered as bioindicators. Under anaerobic or low oxygen conditions, the rhodoquinol-dependent pathway has been reported in the species from the class Heterotrichea. With the help of RNA sequencing (RNAseq) data, Spirostomum spp., are suitable for deep molecular investigations on rquA for rhodoquinone (RQ) biosynthesis. In this study, Spirostomum ambiguum, Spirostomum subtilis, and Spirostomum teres collected from densely vegetated freshwater habitat in Fuzhou, China, explored the evidence of rquA. Based on transcriptome analysis, two to three RquA proteins were identified in S. ambiguum, S. teres, and S. subtilis, respectively. The presence of a key Motif-I of RquA and mitochondrial targeting signals (MTS), also confirmed the identity of these as RquA. Furthermore, Spirostomum RquA proteins could be sorted into two groups based on their conserved amino acid (CAA) residues. Phylogenetic analysis also exhibited RquA division into two subclades contained RquA1 and RquA2/RquA3 and supports two to three paralogs of rquA genes in the genomes Spirostomum spp. Additional transcriptomes and genomes analysis of Blepharisma spp., and Stentor spp., respectively, also revealed at least two paralogs of rquA in members of the class Heterotrichea. The present study provides evidence for the presence of RquA and rhodoquinol dependent fumarate reduction pathway in Spirostomum species potentially use to respire in the oxygen-depleted habitats and two to three diverse rquA genes.

Dynamically Long-Term Imaging of Cellular RNA by Fluorescent Carbon Dots with Surface Isoquinoline Moieties and Amines.

Cellular RNA dynamics are closely associated with a vast range of physiological processes that are mostly long-lasting. To uncover the association between RNA dynamics and these processes, fluorescent RNA probes with high specificity, photostability, and biocompatibility are compulsory. Herein, a series of fluorescent carbon dots (CDs) have been prepared by one-pot hydrothermal treatment of o-, m-, or p-phenylenediamines with triethylenetetramine. Only CDs derived from the meta precursor ( m-CDs) with excellent photostability and biocompatibility can specifically bind to cellular RNA, allowing successfully long-term (up to 3 days) monitoring of RNA dynamics during cell apoptosis, mitosis, and proliferation. This RNA affinity can be attributed to the isoquinoline moieties and amines on the surface of m-CDs, which can bind to RNA through π-π stacking and electrostatic bonding, respectively. The cellular internalization of m-CDs is time-, temperature-, ATP-, caveolar, and microtubule-dependent. Additionally, investigations on the in vivo behavior of m-CD suggest that they can be efficiently and rapidly excreted from the zebrafish larvae body after 48 h. Our results provide a powerful tool for clarifying complex relationships between RNA dynamics and basic biological processes, disease development, or drug interactions.

Bioinformatic analyses of zona pellucida genes in vertebrates and their expression in Nile tilapia.

Zona pellucida (ZP) genes encode ZP glycoproteins which constitute the coat surrounding oocytes and early embryos. Genome-wide identification of ZP genes is still lacking in vertebrates, especially in fish species. Herein, we conducted bioinformatic analyses of the ZP genes of the Nile tilapia and other vertebrates. Totally 16, 9, 17, 27, 21, 20, 26, 19, 14,11, 24, 17, 9, 18, 8, 11, 9, 8, 5, and 4 ZP genes belonging to 5 subfamilies (ZPA, ZPB, ZPC, ZPD, and ZPAX) were found in the sea lamprey, elephant shark, coelacanth, spotted gar, zebrafish, medaka, stickleback, Nile tilapia, Amazon molly, platyfish, seahorse, Northern snakehead, cavefish, tetraodon, clawed frog, turtle, chicken, platypus, kangaroo rat, and human genomes, respectively. The expansion of ZP genes in basal vertebrates was mainly achieved by gene duplication of ZPB, ZPC, and ZPAX subfamilies, while the shrink of ZP gene number in viviparous mammals was achieved by keeping only one copy of the ZP genes in each subfamily or even secondary loss of some subfamilies. The number of ZP gene is related to the environment where the eggs are fertilized and the embryos develop in vertebrates. Transcriptomic analysis showed that 14 ZP genes were expressed in the ovary of Nile tilapia, while two (ZPB2b and ZPC2) were highly expressed in the liver. On the other hand, ZPB1a and ZPB2c were not found to be expressed in any tissue or at any developmental stage of the gonads examined. In the ovary, the expression of ZP genes started from 30 dah (days after hatching), significantly upregulated at 90 dah and maintained this level at 180 dah. The expression of ZPC2 in the liver and ZPC5-2 and ZPAX1 in the ovary was confirmed by in situ hybridization. The ovary- and liver-expressed ZP genes are expressed coordinately with oocyte growth in tilapia.

Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia.

Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods. Further expansion of the members to ~14 (9 Pc and 5 Hp1) was observed in teleosts due to the third round genome duplication (3R). Based on transcriptome data from eight adult tilapia tissues, most of the Cbxs were found to be dominantly expressed in the brain, testis, ovary and heart. Analyses of the gonadal transcriptome data from four developmental stages revealed that all Cbxs were expressed in both ovary and testis except Cbx7b, with significant increase of the total and average RPKM from 5 to 90dah (days after hatching). By in situ hybridization, the three most highly and sexual dimorphically expressed Cbx genes in gonads, Cbx1b, Cbx3a and Cbx5, were found to be expressed in phase I and II oocytes of the ovary, and in secondary spermatocytes (Cbx1b and Cbx3a) and spermatids (Cbx5) of the testis. Our results revealed the evolution of Cbx genes and indicated a potential role of Cbxs in epigenetic regulation of gametogenesis.

Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation.

BACKGROUND: MicroRNAs (miRNAs) represent a second regulatory network that has important effects on gene expression and protein translation during biological process. However, the possible role of miRNAs in the early stages of fish sex differentiation is not well understood. In this study, we carried an integrated analysis of miRNA and mRNA expression profiles to explore their possibly regulatory patterns at the critical stage of sex differentiation in tilapia. RESULTS: We identified 279 pre-miRNA genes in tilapia genome, which were highly conserved in other fish species. Based on small RNA library sequencing, we identified 635 mature miRNAs in tilapia gonads, in which 62 and 49 miRNAs showed higher expression in XX and XY gonads, respectively. The predicted targets of these sex-biased miRNAs (e.g., miR-9, miR-21, miR-30a, miR-96, miR-200b, miR-212 and miR-7977) included genes encoding key enzymes in steroidogenic pathways (Cyp11a1, Hsd3b, Cyp19a1a, Hsd11b) and key molecules involved in vertebrate sex differentiation (Foxl2, Amh, Star1, Sf1, Dmrt1, and Gsdf). These genes also showed sex-biased expression in tilapia gonads at 5 dah. Some miRNAs (e.g., miR-96 and miR-737) targeted multiple genes involved in steroid synthesis, suggesting a complex miRNA regulatory network during early sex differentiation in this fish. CONCLUSIONS: The sequence and expression patterns of most miRNAs in tilapia are conserved in fishes, indicating the basic functions of vertebrate miRNAs might share a common evolutionary origin. This comprehensive analysis of miRNA and mRNA at the early stage of molecular sex differentiation in tilapia XX and XY gonads lead to the discovery of differentially expressed miRNAs and their putative targets, which will facilitate studies of the regulatory network of molecular sex determination and differentiation in fishes.

The complete mitogenome of Tanakia himantegus (Cypriniformes; Cyprinidae).

The complete mitochondrial genome was sequenced from one of the endemic bitterling fish in China. The mitochondrial genome sequence was 16,575 bp in size, and the gene order and contents were identical with the species of the same subfamily like T. lanceolata, T. limbata, Acheilognathus macropterus and A. yamatsutae. Five genes (COII, COIII, ND3, ND6, and CYTB) had an incomplete stop codon. Base composition of the genome is A (29.2%), T (27.4%), C (26.2%), and G (17.2%) with an A+T-rich feature (56.6%) as that of other vertebrate mitochondrial genomes.

Genome-wide identification, evolution and expression analysis of nuclear receptor superfamily in Nile tilapia, Oreochromis niloticus.

The nuclear receptor (NR) superfamily, which is divided into 7 subfamilies, constitutes one of the largest classes of transcription factors. In this study, through comprehensive database search, we identified all NRs (including 4 novel members) from the tilapia (75), common carp (137), zebrafish (73), fugu (73), tetraodon (72), stickleback (70), medaka (69), coelacanth (55), spotted gar (51) and elephant shark (50). For 21 NRs, two duplicates were found in teleosts, while only one in tetrapods. These duplicates, except those of DAX1, SHP and GCNF found in the elephant shark, were derived from 3R (third round of genome duplication). The linkage duplication of 5 syntenic blocks (comprising 14 duplicated NR couples) in teleosts further supported their 3R origin. Based on transcriptome data from adult tilapia, 53 NRs were found to be expressed in more than one tissue (brain, head kidney, heart, liver, kidney, muscle, ovary and testis), and 4 were tissue-specific, indicating their essential roles in the corresponding tissue. Based on the XX and XY gonadal transcriptome data from four developmental stages, 65 NRs were detected in gonads, with 21, 31, 11 and 29 expressed sexual dimorphically at 5, 30, 90 and 180days after hatching, respectively. The expression of four selected genes was examined by in situ hybridization (ISH) and quantitative PCR (qPCR) to validate the spatial and temporal expression profiles of NRs. Comparative analyses of the expression profiles of duplicated NRs revealed divergence in gene expression as well as gene function. Our results demonstrated that NRs may play important roles in sex determination and gonadal development in teleosts.

Retinoic acid homeostasis through aldh1a2 and cyp26a1 mediates meiotic entry in Nile tilapia (Oreochromis niloticus).

Meiosis is a process unique to the differentiation of germ cells. Retinoic acid (RA) is the key factor controlling the sex-specific timing of meiotic initiation in tetrapods; however, the role of RA in meiotic initiation in teleosts has remained unclear. In this study, the genes encoding RA synthase aldh1a2, and catabolic enzyme cyp26a1 were isolated from Nile tilapia (Oreochromis niloticus), a species without stra8. The expression of aldh1a2 was up-regulated and expression of cyp26a1 was down-regulated before the meiotic initiation in ovaries and in testes. Treatment with RA synthase inhibitor or disruption of Aldh1a2 by CRISPR/Cas9 resulted in delayed meiotic initiation, with simultaneous down-regulation of cyp26a1 and up-regulation of sycp3. By contrast, treatment with an inhibitor of RA catabolic enzyme and disruption of cyp26a1 resulted in earlier meiotic initiation, with increased expression of aldh1a2 and sycp3. Additionally, treatment of XY fish with estrogen (E2) and XX fish with fadrozole led to sex reversal and reversion of meiotic initiation. These results indicate that RA is indispensable for meiotic initiation in teleosts via a stra8 independent signaling pathway where both aldh1a2 and cyp26a1 are critical. In contrast to mammals, E2 is a major regulator of sex determination and meiotic initiation in teleosts.

Isolation of doublesex- and mab-3-related transcription factor 6 and its involvement in spermatogenesis in tilapia.

The dmrt6 gene has been isolated from tetrapods and recently from a coelacanth, Latimeria chalumnae. Its evolutionary history and exact function remain unclear. In the present study, dmrt6 was isolated from Perciformes (five cichlids and stickleback), Siluriformes (southern catfish), and Lepisosteiformes (spotted gar). Syntenic and phylogenetic analyses indicated that dmrt6 experienced gene transposition after the divergence of teleosts from other bony fish as gene loci surrounding dmrt6 were conserved among teleosts (but was completely different from gene loci surrounding dmrt6 in tetrapods and spotted gar), while these gene loci were conserved among nonteleost species. Real-time PCR and in situ hybridization revealed that dmrt6 was highly expressed in the XY gonads from 90 days after hatching (dah) onward and was observed exclusively in spermatocytes of the testes in tilapia. Dmrt6 knockout by CRISPR/Cas9 resulted in fewer spermatocytes, down-regulated Cyp11b2 in testes, and consequently produced a lower level of serum 11-ketotestosterone (11-KT) in Dmrt6-deficient XY fish compared with the XY control at 120 dah. From 150 to 180 dah, spermatogenesis gradually recovered, and cyp11b2 expression and serum 11-KT level were restored to the same levels as those of the XY control fish. In addition, a Dmrt6 mutation was observed in genomic DNA of sperm of G0 mutant fish and F1 fish. Taken together, our data suggest that dmrt6 also exists in bony fish. Its absence in most fish genomes was probably due to incomplete sequencing and/or secondary loss. The dmrt6 gene is highly expressed in spermatocytes and is involved in spermatogenesis in tilapia.

Genome-wide identification, phylogeny, and gonadal expression of fox genes in Nile tilapia, Oreochromis niloticus.

The fox genes play important roles in various biological processes, including sexual development. In the present study, we isolated 65 fox genes, belonging to 18 subfamilies named A-R, from Nile tilapia through genome-wide screening. Twenty-four of them have two or three (foxm1) copies. Furthermore, 16, 25, 68, and 45 fox members were isolated from nematodes, protochordates, teleosts, and tetrapods, respectively. Phylogenetic analyses indicated fox gene family had undergone three expansions parallel to the three rounds of genome duplication during evolution. We also analyzed the clustered fox genes and found that apparent linkage duplication existed in teleosts, which further supported fish-specific genome duplication hypothesis. In addition, species- and lineage-specific duplication is another reason for fox gene family expansion. Based on the four pairs of XX and XY gonadal transcriptome data from four critical developmental stages, we analyzed the expression profile of all fox genes and identified sexually dimorphic fox genes at each stage. All fox genes were detected in gonads, with 15 of them at the background expression level (total read per kb per million reads, RPKM < 10), 29 at moderate expression level (10 < total RPKM < 100), and 21 at high expression level (total RPKM > 100). There are 27, 24, 28, and 9 sexually dimorphic fox genes at 5, 30, 90, and 180 days after hatching (dah), respectively. foxq1a, foxf1, foxr1, and foxr1 were identified as the most differentially expressed genes at each stage. foxl2 was characterized as XX-dominant gene, while foxd5, foxi3, foxn3, foxj1a, foxj3b, and foxo6b were characterized as XY-dominant genes. qPCR and in situ hybridization of foxh1 and foxj1a were performed to confirm the expression profiles and to validate the transcriptome data. Our results suggest that fox genes might play important roles in sex determination and gonadal development in teleosts.