Butter clam genome assembly and analysis reveals the historical adaptation of shellfish genome to changes in the marine environment

Purple butter clam (Saxidomus purpuratus) is an economically important bivalve shellfish. This species belongs to the subclass Heterodonta that diverged in calcite seas with low magnesium concentrations. We sequenced and assembled its genome and performed an evolutionary comparative analysis. A total of 911 Mb assembly of S. purpuratus was anchored into 19 chromosomes and a total of 48,090 protein-coding genes were predicted. We identified its repeat-based expanded genes that are associated with the sodium/potassium-exchange ATPase complex. In addition, different types of ion transporters were enriched in the common ancestor of Heterodonta (calcium, sulfate, and lipid transporters) and the specific evolution of S. purpuratus (calcium and sodium transporters). These differences seem to be related to the divergence times of Heterodonta (calcitic sea) and Veneraidea (aragonitic sea). Furthermore, we analyzed the evolution of scavenger receptor (SR) proteins in S. purpuratus, which are involved in a wide range of immune responses, and compared them to the closely related Cyclina sinensis. We showed that a small number of SR proteins, exhibited collinearity between the two genomes, which is indicative of independent gene evolution. Our genomic study provides an evolutionary perspective on the genetic diversity of bivalves and their adaptation to historical changes in the marine environment.

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The draft genome sequence of the grove snail Cepaea nemoralis

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa071 ◽

2021 ◽

Vol 11 (2) ◽

Author(s):

Suzanne V Saenko ◽

Dick S J Groenenberg ◽

Angus Davison ◽

Menno Schilthuizen

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Agricultural Pests ◽

Shell Color ◽

Protein Coding ◽

Cepaea Nemoralis ◽

Edible Species ◽

Wide Range ◽

In Captivity ◽

Long Read

Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

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Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii

Phytopathology ◽

10.1094/phyto-07-12-0151-r ◽

2013 ◽

Vol 103 (5) ◽

pp. 479-487 ◽

Cited By ~ 6

Author(s):

Efrén Remesal ◽

Blanca B. Landa ◽

María del Mar Jiménez-Gasco ◽

Juan A. Navas-Cortés

Keyword(s):

Rna Polymerase Ii ◽

Sequence Variation ◽

Geographic Origin ◽

Sclerotium Rolfsii ◽

Nuclear Ribosomal Dna ◽

Causal Organism ◽

Protein Coding ◽

Protein Coding Genes ◽

Wide Range ◽

Mycelial Compatibility

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.

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Meiotic expression of human ornithine transcarbamylase in the testes of transgenic mice

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1821-1825.1988 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1821-1825

Author(s):

K A Kelley ◽

J W Chamberlain ◽

J A Nolan ◽

A L Horwich ◽

F Kalousek ◽

...

Keyword(s):

Transgenic Mice ◽

Fusion Gene ◽

Regulatory Region ◽

Transgenic Animals ◽

Ornithine Transcarbamylase ◽

Regulatory Sequences ◽

Base Pairs ◽

Protein Coding ◽

Wide Range ◽

Flanking Sequences

In an attempt to use mouse metallothionein-I (mMT-I) regulatory sequences to direct expression of human ornithine transcarbamylase in the liver of transgenic animals, fusion genes joining either 1.6 kilobases or 185 base pairs of the mMT-I regulatory region to the human ornithine transcarbamylase protein-coding sequence were used to produce transgenic mice. In mice carrying the fusion gene with 1.6 kilobases of the mMT-I 5'-flanking sequences, transgene expression was observed in a wide range of tissues, but, unexpectedly, expression in liver was never observed. Surprisingly, in mice carrying the fusion gene regulated by only 185 base pairs of the mMT-I 5'-flanking sequences, the transgene was expressed exclusively in male germ cells during the tetraploid, pachytene stage of meiosis.

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Jujube Phenology, Pollen Germination, and Two Unique Germplasm Resources in New Mexico

HortScience ◽

10.21273/hortsci12512-17 ◽

2018 ◽

Vol 53 (1) ◽

pp. 23-27 ◽

Cited By ~ 1

Author(s):

Shengrui Yao

Keyword(s):

United States ◽

New Mexico ◽

Pollen Germination ◽

Germination Rate ◽

The United States ◽

Germplasm Resources ◽

Male Sterile ◽

Science Center ◽

Genomic Study ◽

Wide Range

Jujube (Ziziphus jujuba Mill.) originated in China and grows well in a wide range of areas in the United States, especially the southwest. New Mexico State University’s Sustainable Agriculture Science Center has imported and collected over 50 jujube cultivars and conducted a series of jujube-related research projects. In this study, jujube phenology and pollen germination in New Mexico were investigated and two unique germplasm resources were reported. Jujubes leafed out 4–8 weeks later than most pome and stone fruits and bloomed 2–3 months later than apricots, peaches, and apples. It can avoid late frosts in most years in northern New Mexico and, thus, produce a crop more reliably than traditional fruit crops in the region. For the 48 cultivars tested for pollen germination, the germination rates ranged from 0% to 75% depending on the cultivar and year. ‘September Late’ had the highest pollen germination rate each year among all cultivars tested from 2012 to 2014, whereas ‘GA866’, ‘Maya’, and ‘Sherwood’ had the lowest. ‘Zaocuiwang’ was the first reported male-sterile jujube cultivar in the United States, and this character was consistent from year to year and, thus, it would be a valuable cultivar for jujube breeding. Cultivar Yu had pseudo-flowers which never bloomed or set fruit. It would be a useful germplasm as special landscape trees or for genomic study of jujube flowering-related genes.

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Intercomparison of Phytoplankton functional types dynamics from satellite observations

10.5194/egusphere-egu21-9855 ◽

2021 ◽

Author(s):

Marine Bretagnon ◽

Séverine Alvain ◽

Astrid Bracher ◽

Philippe Garnesson ◽

Svetlana losa ◽

...

Keyword(s):

Remote Sensing ◽

Marine Environment ◽

Model Simulation ◽

Chlorophyll Concentration ◽

Satellite Observations ◽

Global Ocean ◽

Ocean Colour ◽

Marginal Seas ◽

Functional Types ◽

Wide Range

Copernicus marine environment monitoring service (CMEMS) gives users access to a wide range of ocean descriptors. Both physics and biogeochemistry of the marine environment can be studied with complementary source of data, such as in situ data, modelling output and satellite observations at global scale and/or for European marginal seas. Among the ocean descriptors supplied as part of CMEMS, phytoplankton functional types (PFTs) describe the phytoplanktonic composition at global level or over European marginal seas. Studied phytoplankton assemblage is particularly important as it is the basis of the marine food-web. Composition of the first trophic level is a valuable indicator to infer the structure of the ecosystem and its health. Over the last decades, ocean colour remote sensing has been used to estimate the phytoplanktonic composition. The algorithms developed to estimate PFTs composition based on ocean colour observation can be classified in three categories: the spectral approaches, the abundance-based approaches (derived from the chlorophyll concentration) and the ecological approaches. The three approaches can lead to differences or, conversely, to similar patterns. Difference and similarity in PFTs estimation from remote sensing is a useful information for data assimilation or model simulation, as it provides indications on the uncertainties/variability associated to the PFT estimates. Indeed, PFT estimates from satellite observations are increasingly assimilated into ecological models to improve biogeochemical simulations, what highlights the importance to get an index or at least information describing the validity range of such PFTs estimates.In this study, four algorithms (two abundance-based, and two spectral approaches) are compared. The aim of this study is to compare the related PFT products spatially and temporally, and to study the agreement of their derived PFT phenology. This study proposes also to compare PFT algorithms developed for the global ocean with those developed for specific regions in order to assess the potential strength and weakness of the different approaches. Once similarities and discrepancies between the different approaches are assessed, this information could be used by model to give an interval of confidence in model simulation.

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The High Frequency coastal radar network in the Mediterranean: joint efforts towards a fully operational implementation

10.5194/egusphere-egu21-16311 ◽

2021 ◽

Author(s):

Pablo Lorente ◽

Keyword(s):

Marine Environment ◽

High Frequency ◽

Production Management ◽

Hot Spot ◽

Coastal Areas ◽

Coastal Hazards ◽

Current Status ◽

Wide Range ◽

The Mediterranean

The Mediterranean Sea is considered a relevant geostrategic region and a prominent climate change hot spot. This semi-enclosed basin has been the subject of abundant studies due to its vulnerability to sea-level rise and other coastal hazards. With the steady advent of new technologies, a growing wealth of observational data are nowadays available to efficiently monitor the sea state and properly respond to socio-ecological challenges and stakeholder needs, thereby strengthening the community resilience at multiple scales.Nowadays, High-Frequency radar (HFR) is a worldwide consolidated land-based remote sensing technology since it provides, concurrently and in near real time, fine-resolution maps of the surface circulation along with (increasingly) wave and wind information over broad coastal areas. HFR systems present a wide range of practical applications: maritime safety, oil spill emergencies, energy production, management of extreme coastal hazards. Consequently, they have become an essential component of coastal ocean observatories since they offer a unique dynamical framework that complement conventional in-situ observing platforms. Likewise, within the frame of the Copernicus Marine Environment Monitoring Service (CMEMS), HFR are valuable assets that play a key pivotal role in both the effective monitoring of coastal areas and the rigorous skill assessment of operational ocean forecasting systems.The present work aims to show a panoramic overview not only of the current status of diverse Mediterranean HFR systems, but also of the coordinated joint efforts between many multi-disciplinary institutions to establish a permanent HFR monitoring network in the Mediterranean, aligned with European and global initiatives. In this context, it is worth highlighting that many of the Mediterranean HFR systems are already integrated into the European HFR Node, which acts as central focal point for data collection, homogenization, quality assurance and dissemination and promotes networking between EU infrastructures and the Global HFR network.Furthermore, priority challenges tied to the implementation of a long-term, fully integrated, sustainable operational Mediterranean HFR network are described. This includes aspects related to the setting up of such a system within the broader framework of the European Ocean Observing System (EOOS), and a long-term financial support required to preserve the infrastructure core service already implemented. Apart from the technological challenges, the enhancing of the HFR data discovery and access, the boosting of the data usage as well as the research integration must be achieved by building synergies among academia, management agencies, state government offices, intermediate and end users. This would guarantee a coordinated development of tailored products that meet the societal needs and foster user uptake, serving the marine industry with dedicated smart innovative services, along with the promotion of strategic planning and informed decision-making in the marine environment.

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The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽

10.3390/molecules24020261 ◽

2019 ◽

Vol 24 (2) ◽

pp. 261 ◽

Cited By ~ 8

Author(s):

Yongfu Li ◽

Steven Paul Sylvester ◽

Meng Li ◽

Cheng Zhang ◽

Xuan Li ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Genome Structure ◽

Phylogenetic Reconstruction ◽

Strong Support ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Critically Endangered Species ◽

Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

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MicroRNAs: Crucial Regulators of Stress

MicroRNA ◽

10.2174/2211536608666190625120127 ◽

2020 ◽

Vol 9 (2) ◽

pp. 93-100 ◽

Cited By ~ 1

Author(s):

Rabih Roufayel ◽

Seifedine kadry

Keyword(s):

Rna Polymerase Ii ◽

Lymphoproliferative Disease ◽

Lymphocytic Leukemia ◽

Lung Tumorigenesis ◽

Protein Coding ◽

Mrna Targets ◽

B Cell Malignancy ◽

Potential Binding ◽

Wide Range ◽

Cancer Types

Background: Signaling pathways including gene silencing, cellular differentiation, homeostasis, development and apoptosis are regulated and controlled by a wide range of miRNAs. Objective: Due to their potential binding sites in human-protein coding genes, many studies have also linked their altered expressions in various cancer types making them tumor suppressors agents. Methods: Moreover, each miRNA is predicted to have many mRNA targets indicating their extensive regulatory role in cell survival and developmental processes. Nowadays, diagnosis of early cancer stage development is now dependent on variable miRNA expression levels as potential oncogenic biomarkers in validating and targeting microRNAs for cancer therapy. Results: As the majority of miRNA, transcripts are derived from RNA polymerase II-directed transcription, stress response could result on a general reduction in the abundance of these transcripts. Over expression of various microRNAs have lead to B cell malignancy, potentiated KrasG12Dinduced lung tumorigenesis, chronic lymphocytic leukemia, lymphoproliferative disease and autoimmunity. Conclusion: Altered miRNA expressions could have a significant impact on the abundance of proteins, making them attractive candidates as biomarkers for cancer detection and important regulators of apoptosis.

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LncExpDB: an expression database of human long non-coding RNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa850 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D962-D968 ◽

Cited By ~ 2

Author(s):

Zhao Li ◽

Lin Liu ◽

Shuai Jiang ◽

Qianpeng Li ◽

Changrui Feng ◽

...

Keyword(s):

Expression Profiles ◽

Biological Functions ◽

Protein Coding ◽

Web Interfaces ◽

Functional Studies ◽

Protein Coding Genes ◽

Genes Expression ◽

Wide Range ◽

Non Coding Rnas ◽

User Friendly

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

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Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Planta ◽

10.1007/s00425-020-03480-5 ◽

2020 ◽

Vol 252 (5) ◽

Cited By ~ 2

Author(s):

Li Chen ◽

Qian-Hao Zhu ◽

Kerstin Kaufmann

Keyword(s):

Stress Responses ◽

Translational Regulation ◽

Molecular Mechanisms ◽

Functional Characterization ◽

Reproductive Organs ◽

Gene Activity ◽

Protein Coding ◽

Wide Range ◽

Non Coding Rnas ◽

Coding Potential

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

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