The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification.

Introduction: Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety. Methods: The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussion: The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium. Conclusion: Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.

Nonvisual system-mediated body color change in fish reveals nonvisual function of Opsin 3 in skin.

Body-color changes in many poikilothermic animals can occur quickly. This color change is generally initiated by visual system, followed by neuromuscular or neuroendocrine control. We have previously showed that the ventral skin color of the large yellow croaker (Larimichthys crocea) presents golden yellow in dark environment and quickly changes to silvery white in light environment. In the present study, we found that the light-induced whitening of ventral skin color was independent of visual input. Using light-emitting diode sources of different wavelength with same luminance (150 lx) but different absolute irradiance (0.039-0.333 mW/cm2), we further found that the blue light (λmax = 480 nm, 0.107 mW/cm2) is more effectively in induction of whitening of ventral skin color in compare with other light sources. Interestingly, the result of RT-PCR showed opsin 3 transcripts expressed in xanthophores. Recombinant protein of Opsin 3 with 11-cis retinal formed functional blue-sensitive pigment, with an absorption maximum at 468 nm. The HEK293T cells transfected with Opsin 3 showed a blue light-evoked Ca2+ response. Knock-down of Opsin 3 expression blocked the light-induced xanthosomes aggregation in vitro. Moreover, the light-induced xanthosomes aggregation was mediated via Ca2+-PKC and Ca2+-CaMKII pathways, and relied on microtubules and dynein. Decrease of cAMP levels was a prerequisite for xanthosomes aggregation. Our results provide a unique organism model exhibiting light-induced quick body color change, which was independent of visual input but rather rely on non-visual function of Opsin 3 within xanthophore.

Co-packaged optics (CPO): status, challenges, and solutions.

Due to the rise of 5G, IoT, AI, and high-performance computing applications, datacenter traffic has grown at a compound annual growth rate of nearly 30%. Furthermore, nearly three-fourths of the datacenter traffic resides within datacenters. The conventional pluggable optics increases at a much slower rate than that of datacenter traffic. The gap between application requirements and the capability of conventional pluggable optics keeps increasing, a trend that is unsustainable. Co-packaged optics (CPO) is a disruptive approach to increasing the interconnecting bandwidth density and energy efficiency by dramatically shortening the electrical link length through advanced packaging and co-optimization of electronics and photonics. CPO is widely regarded as a promising solution for future datacenter interconnections, and silicon platform is the most promising platform for large-scale integration. Leading international companies (e.g., Intel, Broadcom and IBM) have heavily investigated in CPO technology, an inter-disciplinary research field that involves photonic devices, integrated circuits design, packaging, photonic device modeling, electronic-photonic co-simulation, applications, and standardization. This review aims to provide the readers a comprehensive overview of the state-of-the-art progress of CPO in silicon platform, identify the key challenges, and point out the potential solutions, hoping to encourage collaboration between different research fields to accelerate the development of CPO technology.

Characteristics of the complete chloroplast genome of Saxifragaceae species Bergenia purpurascens (Hook. f. et Thoms.) Engl.

Bergenia purpurascens (Hook. f. et Thoms.) Engl. is one species of traditional Chinese medicinal plant. This is the first publication of its complete chloroplast (cp) genome. The whole cp genome has 157,246 base pairs in length with 132 annotated genes, of which were 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. According to the phylogenetic study, B. purpurascens and Bergenia scopulosa T. P. Wang. 1974 had a sister relationship. This genomic data and conclusions from B. purpurascens phylogenetic research will provide useful information and throw light on more in-depth investigations of the systematics and evolutionary patterns of Saxifragaceae.

Sequencing and analysis of the complete mitochondrial genome of Hippopus porcellanus.

In this study, the complete mitochondrial genome of Hippopus porcellanus was reported. The whole mitochondrial genome was 21,565bp in length with a typical mitochondrial genomic structure including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). Mitogenome base composition was biased toward A + T content, at 60.3%. A phylogenetic tree based on complete mitogenome sequences revealed that, H. porcellanus is closely related to H. hippopus, both of which belong to the genus Hippopus.

Impaired oocyte maturation and ovulation in membrane progestin receptor (mPR) knockouts in zebrafish.

Accumulating evidence suggest that membrane progestin receptor α (mPRα) is the membrane receptor mediating nongenomic progestin signaling that induces oocyte maturation in teleost. However, the involvement of other members of mPR family in oocyte maturation is still unclear. In this study, we found impaired oocyte maturation in zebrafish lacking mPRα1, mPRα2, mPRß, or mPRγ2. In contrast, no difference was observed in oocyte maturation in the single knockout of mPRγ1, mPRδ, or mPRε. To study possible redundant functions of different mPRs in oocyte maturation, we generated a zebrafish line lacking all seven kinds of mPRs (mprs-/-). We found oocyte maturation was further impaired in mprs-/-. In addition, oocyte ovulation delay was observed in mprs-/- females, which was associated with low levels of nuclear progestin receptor (Pgr), a key regulator for ovulation. We also found reduced fertility in mprs-/- female zebrafish. Furthermore, eggs spawned by mprs-/- females were of poor quality.

Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae).

BACKGROUND: The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. RESULTS: The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N' gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. CONCLUSIONS: This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.

Androstenedione and 17α-methyltestosterone induce early ovary development of Anguilla japonica.

Endocrine effects as 11-ketotestosterone (11-KT), an unaromatizable androgen, regulating the follicles growth in the previtellogenic stage of eel reproduction have been widely elucidated. However, the influence of aromatizable androgens on the brain-pituitary-gonad axis during oogenesis in A. japonica has not been clearly elaborated. In the study, androstenedione (AD) and 17α-methyltestosterone (MT) were employed together to induce ovary development of seven-year-old female Anguilla japonica through feeding or exposure in the migration season. After female A. japonica had been fed with commercial diet containing 5 mg AD and MT kg d-1 body weight respectively for 45 d in fresh water (Trial I), the development of oocytes still remained at the oil droplet stage, but the GSI and follicle diameter increased significantly. The serum 11-KT level and expression of liver vitellogenin mRNA were significantly elevated. After female fish had been exposed to seawater containing 50 µg L-1 AD and MT respectively for 45 d (Trial II), the ovaries of A. japonica almost reached midvitellogenic stage and the GSI and follicle diameter increased significantly. Yolk granular layer was observed in the peripheral ooplasm. The serum 11-KT level maintained consistently low, and the serum E2 level declined significantly to a relatively low level. The expression levels of ovarian arα and cyp19a1, brain (with pituitary together) mGnRH and lhß increased significantly. The results showed that A. japonica in Trial II appeared a higher ovarian development than those in Trial I. These findings indicated that AD and MT increased the oil droplet and enlarged follicle diameter in previtellogenic stage, while the vitellogenesis and gonadotropin release did not occur in Trial I. In Trial II, AD and MT promoted vitellogenesis by stimulating the ovary expression of arα and by up-regulating brain mGnRH and pituitary lhß expression.

Flatfish monophyly refereed by the relationship of Psettodes in Carangimorphariae.

BACKGROUND: The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained. RESULTS: The mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades. Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs. CONCLUSION: Based on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes: The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists.

The complete mitochondrial genome sequence of Siganus sutor (Perciformes: Siganidae).

The complete mitochondrial genome of a marine fish Siganus sutor was completely sequenced by the high throughput sequencing method. This complete mitochondrial genome was 16,497 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of S. sutor is identical to those in typical fishes. Phylogenetic tree based on 13 protein-coding genes shows that Siganidae has a closer phylogenetic relationship to Luvaridae than to Ephippidae or Scatophagidae.

The complete mitochondrial genome sequence of Pelates quadrilineatus (Perciformes: Terapontidae).

The complete mitochondrial genome of marine fish Pelates quadrilineatus was sequenced by the high throughput sequencing method. This genome was 16,823 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of P. quadrilineatus is identical to those of other fishes. Phylogenetic tree based on 13 protein coding genes shows that Terapontidae has a closer phylogenetic relationship to Pentacerotidae than to Chaetodontidae.

The complete mitochondrial genome sequence of the giant clam Tridacna derasa (Tridacnidae: Tridacna).

The complete mitochondrial genome of the giant clam Tridacna derasa was completely sequenced by high-throughput sequencing method. The total length of the complete mitogenome was 20,760bp, including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and a non-coding control region. The base composition of the genome is 28.41% A, 36.92% G, 21.94% G and 12.74% C with a total GC content of 34.68%. Phylogenetic tree based on complete mitogenome sequences revealed that T.derasa was closely related to T.squamosa, both belonging to the Tridacna genus.

The complete mitochondrial genome sequence of Halichoeres nigrescens (Labriformes: Labridae).

The complete mitochondrial genome of marine fish Halichoeres nigrescens was sequenced by the high-throughput sequencing method. The genome is 17,252 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of Halichoeres nigrescens is identical to that of common fishes. Phylogenetic tree based on 13 protein-coding genes shows that Halichoeres nigrescens has a closer phylogenetic relationship to Macropharyngodon negrosensis than to Halichoeres hartzfeldii.

High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.

Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM). The former is predominantly aquatic with less time out of water, while the latter is primarily terrestrial with extended periods of time on land. Within these identified AMPs, 449 sequences are novel; 15 were reported in BP previously; 48 are identically overlapped between BP and PM; 94 were validated by mass spectrometry. Moreover, most AMPs presented differential tissue transcription patterns in the two mudskippers. Interestingly, we discovered two AMPs, hemoglobin ß1 and amylin, with high inhibitions on Micrococcus luteus. In conclusion, our high-throughput screening strategy based on genomic and transcriptomic data opens an efficient pathway to discover new antimicrobial peptides for ongoing development of marine drugs.

Transcriptomic signatures for ovulation in vertebrates.

The central roles of luteinizing hormone (LH), progestin and their receptors for initiating ovulation have been well established. However, signaling pathways and downstream targets such as proteases that are essential for the rupture of follicular cells are still unclear. Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in preovulatory follicular cells collected following the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 3567 genes significantly differentially expressed between WT and Pgr-KO fish (fold change⩾2, p<0.05). Among those, 1543 gene transcripts were significantly more expressed, while 2024 genes were significantly less expressed, in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated that the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved in DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, and nuclear and cell division. Our results indicate that a large set of genes (>3000) is differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs such as growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in the zebrafish model.

Complete mitochondrial genome and phylogenetic analysis of the barred mudskipper Periophthalmus argentilineatus (Perciformes, Gobiidae).

The complete mitochondrial genome sequence of the barred mudskipper Periophthalmus argentilineatus was first determined in this study. The circle genome was 16 509 bp long and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. The nucleotide composition of the heavy strand of P. argentilineatus is 28.28% for A, 27.83% for C, 16.01% for T, and 27.88% for G, with a slight G + C bias of 55.71%. Only the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes were encoded on the light strand, other mitochondrial genes were all encoded on the heavy strand. The mitochondrial gene arrangement of P. argentilineatus is similar to those of most other gobies. The phylogenetic analysis using the neighbor-joining method showed that the kinship between Periophthalmus and Boleophthalmus is closer than those between Periophthalmus and other selected genera. Periophthalmus argentilineatus was clustered into one branch with other four species from the same genus Periophthalmus.

Complete mitochondrial genome of Toxabramis houdemeri (Cypriniformes; Cyprinidae) and its phylogenetic analysis.

Toxabramis houdemeri belongs to the genus Toxabramis in the subfamily of Cultrinae (Cyprinidae). We first determine the complete mitochondrial genome of T. houdemeri in this study. It is 16 618 bp in length, with the base composition on the heavy strand: 30.79% A, 16.61% G, 27.29% C, and 25.31% T. It has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a D-loop region. Phylogenetic analysis showed that T. houdemeri was clustered into one branch of the subfamily of Cultrinae, and closely related to Hemiculter leucisculus. The present study will contribute to genetic resources conservation of T. houdemeri and studying its population genetic structure and phylogenetic relationships.

Complete mitochondrial genome and phylogenetic analysis of the serpent mudskipper Parapocryptes serperaster (Perciformes, Gobiidae): repetitive sequences in the control region.

The complete mitochondrial genome sequence of the serpent mudskipper Parapocryptes serperaster was first determined in this study. The circle genome was 17 243 bp long and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. The nucleotide composition of the heavy strand of P. serperaster is 28.65% for A, 30.07% for C, 25.31% for T, and 15.97% for G, with a slight A + T bias of 53.96%. Only the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes were encoded on the light strand, all other mitochondrial genes were encoded on the heavy strand. A 178-bp tandem repeat, which started from the 827-bp site of the control region, was identified. Like most other gobies, P. serperaster also has the typical vertebrate mitochondrial gene arrangement. The phylogenetic analysis showed that the kinship between Parapocryptes and Boleophthalmus is closer than those between Parapocryptes and other selected genera.

A Modified Model for Assessment for Retreatment with Transarterial Chemoembolization in Chinese Hepatocellular Carcinoma Patients.

PURPOSE: To develop a modified assessment for retreatment with transarterial chemoembolization (mART) score that may be more suitable for Chinese patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS: Chinese patients with HCC who were treated with transarterial chemoembolization in four hospitals were included. A univariate analysis and a multivariate forward Cox regression analysis were used to identify significant prognostic factors of overall survival (OS). A point scoring model was subsequently developed from the training cohort, and the validation process was performed in the validation cohort. RESULTS: The study included 259 patients (124 patients in the training cohort and 135 patients in the validation cohort). Increase in Child-Pugh scores relative to the baseline (P < .001), Barcelona Clinic Liver Cancer (BCLC) stage B before first transarterial chemoembolization (P = .001), and absence of radiologic tumor response (P < .001) were identified as negative prognostic factors for OS and were used to create the mART scores. BCLC staging was substituted for aspartate aminotransferase increase in the mART scores. The mART scores differentiated two groups with distinct prognosis by a cutoff score of 2.5 points (22.9 mo [95% confidence interval (CI), 17.4-28.4] vs 8.9 mo [95% CI, 7.5-10.3] in median survival; P < .001). In the validation cohort, the C index in assessment for retreatment with transarterial chemoembolization (ART) criteria was 0.64, whereas it was 0.82 in mART criteria. CONCLUSIONS: In Chinese patients with HCC, mART score of > 2.5 before second transarterial chemoembolization was associated with poor prognosis. The mART score was probably better validated compared with the ART score.