scholarly journals Diversity, function and evolution of marine invertebrate genomes

2021 ◽  
Author(s):  
Guangyi Fan ◽  
Yaolei Zhang ◽  
Jiahao Wang ◽  
Meiqi Lv ◽  
Haoyang Gao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Hox Genes ◽  
Marine Invertebrates ◽  
Marine Invertebrate ◽  
Human Life ◽  
Gene Families ◽  
Sister Group ◽  
Immune Gene ◽  
Invertebrate Genome

Invertebrates, animals (metazoans) without backbones, encompass ~97% of all animal yet remains understudied. They have provided insights into molecular mechanisms underlying fundamentally identical mechanisms in phylogenetically diverse animals, including vertebrates. Marine invertebrates have long fascinated researchers due to their abundance, diversity, adaptations, and impact on ecosystems and human economies. Here, we report a compendium and appraisal of 190 marine invertebrate genomes spanning 21 phyla, 43 classes, 92 orders, and 134 families. We identify a high proportion and long unit size of tandem repeats, likely contributing to reported difficulties in invertebrate genome assembly. A well-supported phylogenetic tree of marine invertebrates from 974 single-copy orthologous genes resolved topological controversies. We show that Ctenophora is at the basal phylum and Porifera is the sister group of Parahoxozoa; that Xenacoelomorpha is within Bilateria and is the sister group to Protostomia, rejecting three out of four hypotheses in the field; and that Bryozoa is at the basal position of Lophotrochozoa, not grouped into Lophophorata. We also present insights into the genetic underpinnings of metazoans from Hox genes, innate immune gene families, and nervous system gene families. Our marine invertebrate genome compendium provides a unified foundation for studies on their evolution and effects on ecological systems and human life.

Genetic and developmental bases of serial homology in vertebrate limb evolution

Development ◽  
2000 ◽  
Vol 127 (24) ◽  
pp. 5233-5244 ◽  
Author(s):  
I. Ruvinsky ◽  
J.J. Gibson-Brown
Keyword(s):  
Limb Development ◽  
Molecular Mechanisms ◽  
Hox Genes ◽  
Single Gene ◽  
Genetic Data ◽  
Gene Families ◽  
The Body ◽  
Morphological Description ◽  
Developmental Systems ◽  
Vertebrate Limb

Two sets of paired appendages are a characteristic feature of the body plan of jawed vertebrates. While the fossil record provides a good morphological description of limb evolution, the molecular mechanisms involved in this process are only now beginning to be understood. It is likely that the genes essential for limb development in modern vertebrates were also important players during limb evolution. In recent years, genes from a number of gene families have been described that play important roles both in limb induction and in later patterning processes. These advances facilitate inquiries into several important aspects of limb evolution such as their origin, position along the body axis, number and identity. Integrating paleontological, developmental and genetic data, we propose models to explain the evolution of paired appendages in vertebrates. Whereas previous syntheses have tended to focus on the roles of genes from a single gene family, most notably Hox genes, we emphasize the importance of considering the interactions among multiple genes from different gene families for understanding the evolution of complex developmental systems. Our models, which underscore the roles of gene duplication and regulatory ‘tinkering’, provide a conceptual framework for elucidating the evolution of serially homologous structures in general, and thus contribute to the burgeoning field seeking to uncover the genetic and developmental bases of evolution.

scholarly journals Often Overlooked: Understanding and Meeting the Current Challenges of Marine Invertebrate Conservation

2021 ◽  
Vol 8 ◽  
Author(s):  
Emily Yi-Shyuan Chen
Keyword(s):  
Public Perception ◽  
Marine Invertebrates ◽  
Current Knowledge ◽  
Marine Invertebrate ◽  
Human Life ◽  
Habitat Destruction ◽  
Future Research ◽  
Anthropogenic Pressures ◽  
Invertebrate Conservation ◽  
Key Species

Making up over 92% of life in our oceans, marine invertebrates inhabit every zone in the water column, with contributions ranging from ecosystem functioning to socioeconomic development. Compared to charismatic species, marine invertebrates are often underrepresented in IUCN reports and national conservation efforts. Because of this, as climate change intensifies in conjunction with increasing anthropogenic pressures such as habitat destruction, many marine invertebrates are at risk of silently heading toward extinction. However, public perception has shifted in recent years due to the growing awareness of the important roles these invertebrates play in marine and human life. This change may promote greater support for future research and conservation campaigns of key species. This review highlights the importance of marine invertebrates, the environmental and anthropogenic stressors they are currently facing, and the inherent challenges in their successful conservation. Potential solutions to fill the gaps in current knowledge will be also explored in the context of recent globalization and technological advancements. The loss of marine invertebrate biodiversity will have cascading ecological, economic, and sociological repercussions, so compiling key information into a holistic review will add to the conversation of the importance of global marine invertebrate conservation.

scholarly journals Neurotoxicity in Marine Invertebrates: An Update

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 161
Author(s):  
Irene Deidda ◽  
Roberta Russo ◽  
Rosa Bonaventura ◽  
Caterina Costa ◽  
Francesca Zito ◽  
...  
Keyword(s):  
Nervous System ◽  
Marine Invertebrates ◽  
Marine Pollution ◽  
Marine Invertebrate ◽  
High Sensitivity ◽  
Model Systems ◽  
Neural Genes ◽  
Chemical Agents ◽  
Neurotoxic Effects ◽  
Invertebrate Model

Invertebrates represent about 95% of existing species, and most of them belong to aquatic ecosystems. Marine invertebrates are found at intermediate levels of the food chain and, therefore, they play a central role in the biodiversity of ecosystems. Furthermore, these organisms have a short life cycle, easy laboratory manipulation, and high sensitivity to marine pollution and, therefore, they are considered to be optimal bioindicators for assessing detrimental chemical agents that are related to the marine environment and with potential toxicity to human health, including neurotoxicity. In general, albeit simple, the nervous system of marine invertebrates is composed of neuronal and glial cells, and it exhibits biochemical and functional similarities with the vertebrate nervous system, including humans. In recent decades, new genetic and transcriptomic technologies have made the identification of many neural genes and transcription factors homologous to those in humans possible. Neuroinflammation, oxidative stress, and altered levels of neurotransmitters are some of the aspects of neurotoxic effects that can also occur in marine invertebrate organisms. The purpose of this review is to provide an overview of major marine pollutants, such as heavy metals, pesticides, and micro and nano-plastics, with a focus on their neurotoxic effects in marine invertebrate organisms. This review could be a stimulus to bio-research towards the use of invertebrate model systems other than traditional, ethically questionable, time-consuming, and highly expensive mammalian models.

scholarly journals Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian-Hao Zhu ◽  
Warwick Stiller ◽  
Philippe Moncuquet ◽  
Stuart Gordon ◽  
Yuman Yuan ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Wild Type ◽  
Calcium Dependent ◽  
Dependent Protein ◽  
Flanking Region ◽  
Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

scholarly journals Daily Lifestyle and Cutaneous Malignancies

2021 ◽  
Vol 22 (10) ◽  
pp. 5227
Author(s):  
Yu Sawada ◽  
Motonobu Nakamura
Keyword(s):  
Cell Carcinoma ◽  
Molecular Mechanisms ◽  
Skin Diseases ◽  
Human Life ◽  
Lifestyle Factors ◽  
Merkel Cell ◽  
Fundamental Part ◽  
Skin Cancers ◽  
Beneficial Impact ◽  
The Relationship

Daily lifestyle is a fundamental part of human life and its influence accumulates daily in the human body. We observe that a good daily lifestyle has a beneficial impact on our health; however, the actual effects of individual daily lifestyle factors on human skin diseases, especially skin cancers, have not been summarized. In this review, we focused on the influence of daily lifestyle on the development of skin cancer and described the detailed molecular mechanisms of the development or regulation of cutaneous malignancies. Several daily lifestyle factors, such as circadian rhythm disruption, smoking, alcohol, fatty acids, dietary fiber, obesity, and ultraviolet light, are known to be associated with the risk of cutaneous malignancies, malignant melanoma, squamous cell carcinoma, basal cell carcinoma, and Merkel cell carcinoma. Although the influence of some daily lifestyles on the risk of skin cancers is controversial, this review provides us a better understanding of the relationship between daily lifestyle factors and skin cancers.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

On the Chemical Form of Mercury in Edible Fish and Marine Invertebrate Tissue

1992 ◽  
Vol 49 (5) ◽  
pp. 1010-1017 ◽  
Author(s):  
Nicolas S. Bloom
Keyword(s):  
Total Mercury ◽  
Marine Invertebrates ◽  
Marine Invertebrate ◽  
Chemical Form ◽  
Weight Basis ◽  
Atomic Fluorescence Spectrometry ◽  
Atomic Fluorescence ◽  
Saltwater Fish ◽  
Relative Standard ◽  
Wet Weight

Total mercury, monomethylmercury (CH3Hg), and dimethylmercury ((CH3)2Hg) in edible muscle were examined in 229 samples, representing seven freshwater and eight saltwater fish species and several species of marine invertebrates using ultraclean techniques. Total mercury was determined by hot HNO3/H2SO4/BrClldigestion, SnCl2 reduction, purging onto gold, and analysis by cold vapor atomic fluorescence spectrometry (CVAFS). Methylmercury was determined by KOH/methanol digestion using aqueous phase ethylation, cryogenic gas chromatography, and CVAFS detection. Total mercury and CH3Hg concentrations varied from 0.011 to 2.78 μg∙g−1 (wet weight basis, as Hg) for all samples, while no sample contained detectable (CH3)2Hg (<0.001 μg∙g−1 as Hg). The observed proportion of total mercury (as CH3Hg) ranged from 69 to 132%, with a relative standard deviation for quintuplicate analysis of about 10%; nearly all of this variability can be explained by the analytical variability of total mercury and CH3Hg. Poorly homogenized samples showed greater variability, primarily because total mercury and CH3Hg were measured on separate aliquots, which vary in mercury concentration, not speciation. I conclude that for all species studied, virtually ail (>95%) of the mercury present is as CH3Hg and that past reports of substantially lower CH3Hg fractions may have been biased by analytical and homogeneity variability.

Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures

2006 ◽  
Vol 598 (1-2) ◽  
pp. 120-131 ◽  
Author(s):  
Hitoshi Nakagama ◽  
Kumiko Higuchi ◽  
Etsuko Tanaka ◽  
Naoto Tsuchiya ◽  
Katsuhiko Nakashima ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Dna Structures ◽  
G4 Dna ◽  
Short Tandem

scholarly journals Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L.

2021 ◽  
Vol 22 (2) ◽  
pp. 920
Author(s):  
Ling Cheng ◽  
Wanling Min ◽  
Man Li ◽  
Lili Zhou ◽  
Chuan-Chih Hsu ◽  
...  
Keyword(s):  
Glycine Max ◽  
Molecular Mechanisms ◽  
Human Life ◽  
Phosphate Starvation ◽  
Limiting Factor ◽  
Transcriptional Level ◽  
Label Free ◽  
Promoter Regions ◽  
Glycine Max L ◽  
Soybean Plants

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes.

Abrupt mortality of marine invertebrates at the Younger Dryas-Holocene transition in a shallow inlet of the Goldthwait Sea

The Holocene ◽  
2018 ◽  
Vol 28 (12) ◽  
pp. 1894-1908
Author(s):  
Andréanne Bourgeois-Roy ◽  
Hugo Crites ◽  
Pascal Bernatchez ◽  
Denis Lacelle ◽  
André Martel
Keyword(s):  
Mytilus Edulis ◽  
Marine Invertebrates ◽  
Transition Period ◽  
Marine Invertebrate ◽  
Laurentide Ice Sheet ◽  
The North ◽  
Invertebrate Diversity ◽  
Shell Deposit ◽  
The Impact ◽  
Rapid Environmental Change

The late Pleistocene–early Holocene transition period was characterized by rapid environmental change. Here, we investigate the impact of these changes on the marine invertebrates living in a shallow inlet of the post-glacial Goldthwait Sea. The site is located near Baie-Comeau (QC, Canada), where a number of remarkably well-preserved shell deposits are found along the Rivière aux Anglais Valley on the north shore of the St. Lawrence maritime estuary. Seven phyla of marine invertebrates with a minimum of 25 species or taxa were inventoried in a shell deposit, dominated by a community of Hiatella arctica with Mytilus edulis and barnacles composing the subcommunity. The majority of taxa identified in the shell deposit are boreal and sub-Arctic species; however, temperate species that exist today in the St. Lawrence maritime estuary have not been found. Based on marine invertebrate diversity and δ18O(CaCO3) of Mytilus edulis, the water in the shallow inlet of the Goldthwait Sea must have been cold and saline. The range of AMS 14C ages from 15 Mytilus edulis, constrained to 10,900 and 10,690 cal. yr BP, and exceptional state of preservation of adult and juvenile molluscan specimens suggest the abrupt mortality of entire invertebrate communities due to changing hydrodynamic conditions that included the combined effect of freshwater discharge from the receding Laurentide Ice Sheet and rapid isostatic uplift.

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