Additional Duplication Research Articles

Evolutionary dynamics and functional characterization of proximal duplicated sorbitol-6-phosphate dehydrogenase genes in Rosaceae

Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol 6-phosphate dehydrogenase (S6PDH) functions as the pivotal rate-limiting enzyme in sorbitol synthesis. The origin and functional diversification of S6PDH in Rosaceae remain unclear, largely due to the complicated interplay of gene duplications. Here, we investigated the synteny relationships among all identified S6PDH genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage-specific expansion and syntenic conservation of S6PDH across diverse Rosaceae plant lineages. We found that S6PDH can be traced back to a pair of proximal duplicated genes of the common ancestor of the Rosaceae, and the further amplification of S6PDH in the Maleae primarily relies on WGD events in their lineages. In Rosaceae species, multiple copies of the S6PDH gene are preliminarily divided into two main clades (Clade 1 and Clade 2) based on sequence similarity. These clades have evolved to acquire different functional directions. In Clade 1, lineage-specific transposition events in the Amygdaloideae have led to changes in gene expression patterns and promoted lineage evolution. This is mainly characterized by a decrease in enzymatic activity and transcriptional expression in the leaves, but also includes specific functional diversification, such as sustained post-harvest fruit expression and enhanced expression under biotic stress in certain tissues. In contrast, S6PDH in the Rosoideae and Dryadoideae has not undergone additional duplications beyond early proximal duplication. The loss of exons and variations in exon length might the key factor leading to reduced enzymatic activity in the Clade 2 proximal gene pairs. Collectively, our findings illuminate the dynamic nature of S6PDH evolution and reveal the intricate interplay between duplication, transposition, and functional diversification. This work not only contributes valuable insights into the genetic mechanisms underlying sorbitol metabolism but also establish a crucial foundation for future investigations aimed at comprehensively characterizing the variations of sorbitol metabolism across different subfamilies within the Rosaceae family.

Untangling Zebrafish Genetic Annotation: Addressing Complexities and Nomenclature Issues in Orthologous Evaluation of TCOF1 and NOLC1.

Treacher Collins syndrome (TCS) is a genetic disorder affecting facial development, primarily caused by mutations in the TCOF1 gene. TCOF1, along with NOLC1, play important roles in ribosomal RNA transcription and processing. Previously, a zebrafish model of TCS successfully recapitulated the main characteristics of the syndrome by knocking down the expression of a gene on chromosome 13 (coding for Uniprot ID B8JIY2), which was identified as the TCOF1 orthologue. However, database updates renamed this gene as nolc1 and the zebrafish database (ZFIN) identified a different gene on chromosome 14 as the TCOF1 orthologue (coding for Uniprot ID E7F9D9). NOLC1 and TCOF1 are large proteins with unstructured regions and repetitive sequences that complicate alignments and comparisons. Also, the additional whole genome duplication of teleosts sets further difficulty. In this study, we present evidence that endorses that NOLC1 and TCOF1 are paralogs, and that the zebrafish gene on chromosome 14 is a low-complexity LisH domain-containing factor that displays homology to NOLC1 but lacks essential sequence features to accomplish TCOF1 nucleolar functions. Our analysis also supports the idea that zebrafish, as has been suggested for other non-tetrapod vertebrates, lack the TCOF1 gene that is associated with tripartite nucleolus. Using BLAST searches in a group of teleost genomes, we identified fish-specific sequences similar to E7F9D9 zebrafish protein. We propose naming them "LisH-containing Low Complexity Proteins" (LLCP). Interestingly, the gene on chromosome 13 (nolc1) displays the sequence features, developmental expression patterns, and phenotypic impact of depletion that are characteristic of TCOF1 functions. These findings suggest that in teleost fish, the nucleolar functions described for both NOLC1 and TCOF1 mediated by their repeated motifs, are carried out by a single gene, nolc1. Our study, which is mainly based on computational tools available as free web-based algorithms, could help to solve similar conflicts regarding gene orthology in zebrafish.

Novel variants in TECRL leading to catecholaminergic polymorphic ventricular tachycardia.

Pathogenic and likely pathogenic variants in the TECRL gene are known to be associated with recessive catecholaminergic polymorphic ventricular tachycardia 3, which can include prolonged QT intervals (MIM#614021). We report a case of cardiac arrest in a previously healthy adolescent male in the community. The patient was found to have a novel maternally inherited likely pathogenic variant in TECRL (c.915T>G [p.Tyr305Ter]) and an additional 19-kb duplication encompassing multiple exons of TECRL (chr4:65165944-65185287, dup [4q13.1]) not identified in the mother. Genetic results were revealed via rapid whole-genome sequencing, which allowed appropriate treatment and prognostication.

The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species

Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.

Retraction: Naringenin inhibits migration, invasion, induces apoptosis in human lung cancer cells and arrests tumour progression invitro.

Shi X, Luo X, Chen T, Guo W, Liang C, Tang S, Mo J. Naringenin inhibits migration, invasion, induces apoptosis in human lung cancer cells and arrests tumour progression invitro. J Cell Mol Med. 2021; 25: 2563-2571. https://doi.org/10.1111/jcmm.16226 The above article, published online on 1 February 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Stefan N. Constantinescu, and the Foundation for Cellular and Molecular Medicine/John Wiley & Sons Ltd. Following publication, concerns were raised by third parties that portions of Figure1 are identical to Figure1 in another article (1) from a different author group and covering a different research topic. Further investigation confirmed these concerns and revealed additional duplication in Figures1 and 3, overlapping with Figures1 and 2 in (1). The authors of both articles were approached for an explanation but were unable to address the concerns raised. The authors of (1) did not respond, and the authors of this article were unable to provide any underlying data. The retraction has been agreed because of concerns regarding the integrity of the research presented given that the figures were duplicated. (1) Zhang J, Wang R, Cheng L, Xu H. Celastrol inhibit the proliferation, invasion and migration of human cervical HeLa cancer cells through down-regulation of MMP-2 and MMP-9. J Cell Mol Med. 2021; 25: 5335-5338. https://doi.org/10.1111/jcmm.16488.

Retraction: Celastrol inhibit the proliferation, invasion and migration of human cervical HeLa cancer cells through down-regulation of MMP-2 and MMP-9.

Zhang J, Wang R, Cheng L, Xu H. Celastrol inhibit the proliferation, invasion and migration of human cervical HeLa cancer cells through down-regulation of MMP-2 and MMP-9. J Cell Mol Med. 2021;25:5335-5338. doi: 10.1111/jcmm.16488 The above article, published online on 4 May 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Stefan N. Constantinescu, and the Foundation for Cellular and Molecular Medicine/John Wiley & Sons Ltd. Following publication, concerns were raised by third parties that portions of Figure1 are identical to Figure1 presented in another article (1) from a different author group and covering a different research topic. Further investigation confirmed these concerns and revealed additional duplication in Figures1 and 2, overlapping with Figures1 and 3 in (1). The authors of both articles were approached for an explanation but the authors of this article did not respond. The authors of (1) were unable to provide any underlying data. The retraction has been agreed because of concerns regarding the integrity of the research presented given that the figures were duplicated. (1) Shi X, Luo X, Chen T, etal. Naringenin inhibits migration, invasion, induces apoptosis in human lung cancer cells and arrests tumour progression invitro. J Cell Mol Med. 2021;25:2563-2571. doi: 10.1111/jcmm.16226.

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.

We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.

Unraveling the G protein-coupled receptor superfamily in aphids: Contractions and duplications linked to phloem feeding

The G Protein-Coupled Receptor (GPCR) superfamily is the largest and most diverse transmembrane receptor family, playing crucial roles in regulating various physiological processes. As one of the most destructive pests, aphids have been subject to previous studies, which revealed fewer GPCR superfamily members in Acyrthosiphon pisum and Aphis gossypii and the loss of multiple neuropeptide GPCRs. To elucidate the contraction patterns and evolutionary features of the aphid GPCR superfamily, we identified 97, 105, and 95 GPCR genes in Rhopalosiphum maidis, A. pisum, and A. gossypii, respectively. Comparative analysis and phylogenetic investigations with other hemipteran insects revealed a contracted GPCR superfamily in aphids. This contraction mainly occurred in biogenic amine receptors, GABA-B-R, and fz families, and several neuropeptide receptors such as ACPR, CrzR, and PTHR were completely lost. This phenomenon may be related to the parasitic nature of aphids. Additionally, several GPCRs associated with aphid feeding and water balance underwent duplication, including Lkr, NPFR, CCHa1-R, and DH-R, Type A LGRs, but the SK/CCKLR that inhibits feeding was completely lost, indicating changes in feeding genes that underpin the aphid's prolonged phloem feeding behavior. Furthermore, we observed fine-tuning in opsins, with reduced long-wavelength opsins and additional duplications of short-wavelength opsin, likely associated with daytime activity. Lastly, we found variations in the number of mthl genes in aphids. In conclusion, our investigation sheds light on the GPCR superfamily in aphids, revealing its association with diet lifestyle and laying the foundation for understanding and developing control strategies for the aphid GPCR superfamily.

Outcome of Allogeneic Stem Cell Transplantation in FLT3-TKD-Mutated AML - a Study on Behalf of the Acute Leukemia Working Party of the EBMT

Introduction The overall prognostic impact of point mutations in the tyrosine-kinase domain 1 of FLT3 (FLT3-TKD mut) in patients (pts) with acute myelogenous leukemia (AML) remains controversial. Furthermore, co-occurrence of FLT3-TKD mut and mutated nucleophosmin-1 (NPM1 mut) was shown to have a favorable prognostic impact on AML pts receiving conventional chemotherapy. However, little is known about the outcome of AML pts with FLT3-TKD mut with or without co-occurring NPM1 mut treated with allogeneic stem cell transplantation (alloSCT). Patients and Methods This is a retrospective study of the acute leukemia working party (ALWP) of the European Society for Blood and Marrow transplantation (EBMT) investigating the outcome of adult AML pts with FLT3-TKD mut with or without NPM1 mut after first alloSCT using matched sibling (MSD), unrelated (UD) or haploidentical (haplo) donors between 2005 and 2022. All patients were in first or second complete remission (CR1 of CR2). Information on cytogenetic risk was necessary for inclusion. No ex-vivo T-cell depletion (TCD) was allowed. The primary endpoint was leukemia-free survival (LFS) at two years after alloSCT. Secondary endpoints were overall survival (OS), cumulative incidence of relapse (RI), non-relapse mortality (NRM), acute and chronic graft-versus-host disease (GVHD) and GVHD-free, relapse free survival (GRFS). One hundred and eighty-two adult AML pts with FLT3-TKD mut were identified, of which 74 (40.7%) had a co-occurring mutation in NPM1. Median age was 55.1 years (range 18.6-79.1) and 46.7% were male. Median follow-up was 21.4 months [IQR 13.6-28.1]. 78% of the pts were in CR1. Cytogentic risk was favorable, intermediate and adverse in 12.6%, 75.3% and 12.1% of pts, respectively. Additional FLT3 internal tandem duplication (FLT3-ITD) was present in 25.8% of pts. Information on measurable residual disease (MRD) was available for 68.7% of pts, being positive in 48% of these. Karnofsky performance score was < 90% in 21.1%, and hematopoietic cell transplantation-specific comorbidity index (HCT-CI) was >=3 in 28.1% of pts. 69.6% of pts were cytomegalovirus (CMV) positive. Conditioning was myeloablative in 52.8% and reduced intensity in 47.2% of pts. Stem cell donors were MSD, UD and haplo in 25.8%, 55.5% and 18.7% of cases. Stem cell source was bone marrow in 10.4%, peripheral blood in 87.4% and both in 2.2%. In-vivo TCD was performed in 59.2% of pts. GVHD prophylaxis was calcineurin inhibitor-based in 92.2% of pts. Results Engraftment was achieved in 99.4% of pts with a day-60 absolute neutrophil count (ANC) >0.5 x 10 9/L of 97.7% [95% CI: 93.7-99.2]. Day-180 rates of acute GVHD (aGVHD) grade II-IV and grade III-IV were 26.2% (95% CI:19.9-32.9) and 8.1% (95% CI:4.6-12.8), respectively. At two years, rates of total chronic GVHD (cGVHD) and extensive cGVHD were 30% (95% CI: 22.5-38) and 16.6% (95% CI:10.6-23.7), respectively. Two-year LFS and OS were 66.1% (95% CI: 57.6-73.2) and 74% (95% CI: 65.4-80.8), respectively. Two-year RI, NRM and GRFS were 22.5% (95% CI:16-29.8), 11.4% (95% CI: 7-17), and 51.1% (95% CI: 42.4-59.1), respectively. Cause of death was original disease in 47.5%, infection in 27.5%, GVHD in 22.5% and non-SCT related in 2.5% of cases. In univariate analysis the only factor with significant impact on LFS was donor type (haplo [n=34] vs. others, p=0.006). For GRFS, patient CMV negativity (p=0.014) and in-vivo TCD (p=0.01) were significant. Interestingly, co-occurring mutations in FLT3 (FLT3-ITD) or NPM1 were not identified as having a significant impact on LFS or GRFS. Moreover, MRD status before alloSCT was also not shown to have a significant impact on these outcomes. In multivariate analysis of LFS and GRFS, only donor type (haplo [n=34] vs. others) was shown to be significant for both endpoints, hazard ratio (HR) 2.54; 95% CI: 1.4-4.6; p=0.002, and HR 2.01; 95% CI: 1.18-3.41; p=0.01, respectively. Conclusion Acknowledging the limitations of our retrospective study in this rare entity results are encouraging given the high-risk population (median age 55.1 years, CR2 in 22%, co-occurring FLT3-ITD in 25.8%, positive MRD in 48%, HCT CI >=3 in 28.1%). LFS, OS and GRFS rates were 66.1%, 74% and 51.1%, respectively, and both RI and NRM were comparably low with rates of 22.5% and 11.4%, respectively. No positive prognostic impact of co-occurring mutations in FLT3-TKD and NPM1 was detected, unlike what was found for conventional chemotherapy.

PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish.

Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.

Characterization of free fatty acid receptor family in rainbow trout (Oncorhynchus mykiss): towards a better understanding of their involvement in fatty acid signalisation

Since 20 years of research, free fatty acids receptors (FFARs) have received considerable attention in mammals. To date, four FFARs (FFAR1, FFAR2, FFAR3 and FFAR4) are especially studied owing to their physiological importance in various biological processes. This ubiquitist group of G protein-coupled receptors (GPCRs) are majors reports in the key physiological functions such as the regulation of energy balance, metabolism or fatty acid sensing. However, up till date, even some studies were interested in their potential involvement in fatty acid metabolism, no genome investigation of these FFARs have been carried out in teleost fish. Through genome mining and phylogenetic analysis, we identified and characterised 7 coding sequences for ffar2 in rainbow trout whereas no ffar3 nor ffar4 gene have been found. This larger repertoire of ffar2 genes in rainbow trout results from successive additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. A syntenic analysis was used to assign a new nomenclature to the salmonid ffar2 and showed a clear conservation of genomic organisation, further supporting the identity of these genes as ffar2. RT-qPCR was then used to examine, firstly during ontogenesis and secondly on feeding response the expression pattern of ffar1 and ffar2 genes in proximal gut and brain of all trout ffar genes. Overall, this study presents a comprehensive overview of the ffar family in rainbow trout.

A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha

BackgroundTeleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular.ResultsA high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris.ConclusionsWe present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.

Ras protein abundance correlates with Ras isoform mutation patterns in cancer

Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.

Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype inyak.

White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.

A finTRIM member 100 (FTR100) is unique to Otomorpha fish for constitutive regulation of IFN response

Vertebrate interferon (IFN) expression is fine-tuned in order to avoid excessive tissue injury under normal conditions and during virus infection. FinTRIM (fish novel TRIM, FTR) proteins are reported to regulate the fish IFN response. Here, we identify a novel finTRIM gene from yellow catfish (Pelteobagrus fulvidraco), which is sequentially named PfFTR100 according to the nomenclature rule in zebrafish. Genome-wide analyses reveal that FTR100 is unique to Otomorpha fish, with a single copy in spite of additional genome duplication in some fish species. Considering that few of the 99 finTRIM genes identified in zebrafish are conserved in main fish branches and most, such as FTR100, are unique to distinct branches due to lineage-specific expansion of finTRIM genes, we develop a nomenclature for newly cloned finTRIM genes from different fish species. PfFTR100 mRNA is not induced by virus infection, with a relatively high expression level comparable to that of cellular IFN and some IFN-stimulated genes (ISGs) in virally-infected tissues. However, ectopically-expressed PfFTR100 protein is attenuated in virally-infected cells through the proteasomal-dependent pathway. Overexpression of PfFTR100 promotes SVCV replication by downregulating the constitutive and inducible IFN response via a mechanism by which PfFTR100 targets IRF3 and IRF7 to attenuate their mRNA levels rather than their protein levels. Our results indicate that yellow catfish FTR100 is essential for homeostatic regulation of fish tonic IFN response.

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family.

The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.

Meliaceae genomes provide insights into wood development and limonoids biosynthesis.

Meliaceae is a useful plant family owing to its high-quality timber and its many limonoids that have pharmacological and biological activities. Although some genomes of Meliaceae species have been reported, many questions regarding their unique family features, namely wood quality and natural products, have not been answered. In this study, we provide the whole-genome sequence of Melia azedarach comprising 237.16 Mb with a contig N50 of 8.07 Mb, and an improved genome sequence of Azadirachta indica comprising 223.66 Mb with a contig N50 of 8.91 Mb. Moreover, genome skimming data, transcriptomes and other published genomes were comprehensively analysed to determine the genes and proteins that produce superior wood and valuable limonoids. Phylogenetic analysis of chloroplast genomes, single-copy gene families and single-nucleotide polymorphisms revealed that Meliaceae should be classified into two subfamilies: Cedreloideae and Melioideae. Although the Meliaceae species did not undergo additional whole-genome duplication events, the secondary wall biosynthetic genes of the woody Cedreloideae species, Toona sinensis, expanded significantly compared to those of A. indica and M. azedarach, especially in downstream transcription factors and cellulose/hemicellulose biosynthesis-related genes. Moreover, expanded special oxidosqualene cyclase catalogues can help diversify Sapindales skeletons, and the clustered genes that regulate terpene chain elongation, cyclization and modification would support their roles in limonoid biosynthesis. The expanded clans of terpene synthase, O-methyltransferase and cytochrome P450, which are mainly derived from tandem duplication, are responsible for the different limonoid classes among the species. These results are beneficial for further investigations of wood development and limonoid biosynthesis.

Evolution of casein kinase 1 and functional analysis of new doubletime mutants in Drosophila.

Circadian clocks are timing devices that rhythmically adjust organism's behavior, physiology, and metabolism to the 24-h day-night cycle. Eukaryotic circadian clocks rely on several interlocked transcription-translation feedback loops, where protein stability is the key part of the delay between transcription and the appearance of the mature proteins within the feedback loops. In bilaterian animals, including mammals and insects, the circadian clock depends on a homologous set of proteins. Despite mostly conserved clock components among the fruit fly Drosophila and mammals, several lineage-specific differences exist. Here we have systematically explored the evolution and sequence variability of insect DBT proteins and their vertebrate homologs casein kinase 1 delta (CKIδ) and epsilon (CKIε), dated the origin and separation of CKIδ from CKIε, and identified at least three additional independent duplications of the CKIδ/ε gene in Petromyzon, Danio, and Xenopus. We determined conserved regions in DBT specific to Diptera, and functionally tested a subset of those in D. melanogaster. Replacement of Lysine K224 with acidic residues strongly impacts the free-running period even in heterozygous flies, whereas homozygous mutants are not viable. K224D mutants have a temperature compensation defect with longer free-running periods at higher temperatures, which is exactly the opposite trend of what was reported for corresponding mammalian mutants. All DBTs of dipteran insects contain the NKRQK motif at positions 220-224. The occurrence of this motif perfectly correlates with the presence of BRIDE OF DOUBLETIME, BDBT, in Diptera. BDBT is a non-canonical FK506-binding protein that physically interacts with Drosophila DBT. The phylogeny of FK506-binding proteins suggests that BDBT is either absent or highly modified in non-dipteran insects. In addition to in silico analysis of DBT/CKIδ/ε evolution and diversity, we have identified four novel casein kinase 1 genes specific to the Drosophila genus.

A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization.

Japanese eels (Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group δ and ζ genes) and voltage-gated Ca2+ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.

Comprehensive Bioinformatics and Expression Analysis of TCP Transcription Factors in Liriodendron chinense Reveals Putative Abiotic Stress Regulatory Roles

As a magnoliid angiosperm, the Liriodendron chinense (Hamsl) Sarg in the Magnoliaceae family is susceptible to external environmental factors. The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) proteins known for their growth and developmental biological roles have been identified in various plant species but not in the Liriodendron chinense. In this study, 15 TCP genes were identified in the L. chinense genome, and categorized into two classes, termed class I (PCF) and class II (CIN and CYC/TB1). A total of 14 TCP genes were located on the 10 chromosomes, and the remaining one, on a contig. Multispecies phylogenetic tree analysis supported the classification of identified LcTCP genes and exhibited that the expansion of the LcTCP gene family was before the angiosperm evolutionary divergence times. Additional gene duplication investigations revealed a purifying selection pressure during evolution history. Moreover, the LcTCP genes were also observed to have various cis-acting elements related to plant growth and development, phytohormone regulations, and abiotic stress responses. Gene expression pattern analysis also paraded that LcTCP genes play a crucial role in abiotic stress regulations. In particular, LcTCP1 in all stresses investigated. Overall, our findings suggest a pivotal role for the TCP gene family during external environmental stresses in L. chinense. This study will provide valuable information on the identification and function of the LcTCPs during abiotic stresses, paving the way for further research on the functional verification of L. chinense TCPs.