scholarly journals The genome of Shaw’s sea snake (Hydrophis curtus) reveals secondary adaptation to its marine environment

2020 ◽  
Author(s):  
Changjun Peng ◽  
Jin-Long Ren ◽  
Cao Deng ◽  
Dechun Jiang ◽  
Jichao Wang ◽  
...  
Keyword(s):  
Rapid Evolution ◽  
Venom Gland ◽  
Salt Glands ◽  
Protein Coding ◽  
Sea Snake ◽  
Sea Snakes ◽  
Genetic Mechanisms ◽  
Marine Adaptation ◽  
Genomic Regions ◽  
Adaptive Specializations

Abstract The transition of terrestrial snakes to marine life approximately 10 million years ago (Ma) is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs and salt glands yet knowledge on the genetic underpinnings of the transition remain limited. Herein, we report the first genome of Shaw’s sea snake (Hydrophis curtus) and use it to investigate sea snake secondary marine adaptation. A hybrid assembly strategy obtains a high quality genome. Gene family analyses date a pulsed coding-gene expansion to about 20 Ma, and these genes associate strongly with adaptations to marine environments. Analyses of selection pressure and convergent evolution discover the rapid evolution of protein-coding genes, and some convergent features. Additionally, 108 conserved non-coding elements appear to have evolved quickly, and these may underpin the phenotypic changes. Transposon elements may contribute to adaptive specializations by inserting into genomic regions around functionally related coding genes. The integration of genomic and transcriptomic analyses indicates independent origins and different components in sea snake and terrestrial snake venom; the venom gland of the sea snake harbours the highest PLA2 (17.23%) expression in selected elapids and these genes may organize tandemly in the genome. These analyses provide insights into the genetic mechanisms that underlay the secondary adaptation to marine and venom production of this sea snake.

scholarly journals Venom of the Annulated Sea Snake Hydrophis cyanocinctus: A Biochemically Simple but Genetically Complex Weapon

Toxins ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 548
Author(s):  
Hong-Yan Zhao ◽  
Yan Sun ◽  
Yu Du ◽  
Jia-Qi Li ◽  
Jin-Geng Lv ◽  
...  
Keyword(s):  
Marine Environment ◽  
De Novo ◽  
Venom Gland ◽  
Secretory Protein ◽  
Sea Snake ◽  
Sea Snakes ◽  
Venom Toxins ◽  
Low Toxicity ◽  
Venom Evolution ◽  
And Function

Given that the venom system in sea snakes has a role in enhancing their secondary adaption to the marine environment, it follows that elucidating the diversity and function of venom toxins will help to understand the adaptive radiation of sea snakes. We performed proteomic and de novo NGS analyses to explore the diversity of venom toxins in the annulated sea snake (Hydrophis cyanocinctus) and estimated the adaptive molecular evolution of the toxin-coding unigenes and the toxicity of the major components. We found three-finger toxins (3-FTxs), phospholipase A2 (PLA2) and cysteine-rich secretory protein (CRISP) in the venom proteome and 59 toxin-coding unigenes belonging to 24 protein families in the venom-gland transcriptome; 3-FTx and PLA2 were the most abundant families. Nearly half of the toxin-coding unigenes had undergone positive selection. The short- (i.p. 0.09 μg/g) and long-chain neurotoxin (i.p. 0.14 μg/g) presented fairly high toxicity, whereas both basic and acidic PLA2s expressed low toxicity. The toxicity of H. cyanocinctus venom was largely determined by the 3-FTxs. Our data show the venom is used by H. cyanocinctus as a biochemically simple but genetically complex weapon and venom evolution in H. cyanocinctus is presumably driven by natural selection to deal with fast-moving prey and enemies in the marine environment.

scholarly journals Runaway GC Evolution in Gerbil Genomes

2020 ◽  
Vol 37 (8) ◽  
pp. 2197-2210 ◽  
Author(s):  
Rodrigo Pracana ◽  
Adam D Hargreaves ◽  
John F Mulley ◽  
Peter W H Holland
Keyword(s):  
Rapid Evolution ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Genomic Region ◽  
Recombination Rates ◽  
Substitution Pattern ◽  
Substitution Rates ◽  
Protein Coding ◽  
Murine Rodents ◽  
Genomic Regions

Abstract Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.

scholarly journals Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simin Chai ◽  
Ran Tian ◽  
Juanjuan Bi ◽  
Shixia Xu ◽  
Guang Yang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Rapid Evolution ◽  
Genetic Material ◽  
Comparative Genomic ◽  
Testicular Descent ◽  
Ancestral State ◽  
Undescended Testes ◽  
Genomic Analyses ◽  
Genetic Mechanisms ◽  
Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Why Do Centromeres Evolve So Fast: BIR Replication, Hypermutation, Transposition, and Molecular-Drive

2020 ◽  
Author(s):  
William Rice
Keyword(s):  
Rapid Evolution ◽  
Evolutionary Process ◽  
Epigenetic Mark ◽  
Replication Forks ◽  
Nucleotide Substitutions ◽  
Molecular Drive ◽  
Repeat Structure ◽  
Repeat Units ◽  
Initiation Of Replication ◽  
Genomic Regions

Centromeres are among the fastest evolving genomic regions in a diverse array of organisms. The evolutionary process driving this rapid evolution has not been unambiguously established. Here I integrate diverse information to motivate a model in which centromeres evolve rapidly because of their intrinsic molecular phenotype: they tightly bind centromeric proteins throughout the cell cycle. DNA-bound proteins have been shown to cause stalling and collapse of DNA replication forks in many genomic regions, including centromeres. Collapsed replication forks generate one-sided double strand breaks (DSBs) that are repaired by the Break-Induced Repair (BIR) pathway. Here I show why this repair is expected to generate tandem repeat structure and three key features at centromeres: i) increased nucleotide substitution mutation rates, ii) out-of- register re-initiation of replication that leads to indels spanning one or more repeat units, and iii) elevated rates of large and small transpositions within centromeres and between genomic regions. These phenotypes lead to: i) a rapid rate of nucleotide substitutions within a clade of centromeric sequences, ii) continual turnover of monomers within centromeres that fosters molecular-drift and molecular-drive, and iii) recurrent quantum leaps in centromere sequence due to the formation of mosaic monomers and new sequences transposed into non-homologous centromeres. These features are plausibly the major reason centromeres evolve so rapidly. I also speculate on how the DNA sequence of centromeres might perpetually coevolve with the protein sequence of histone CENH3 –the major epigenetic mark of centromeres.

scholarly journals Mutational analysis of driver genes with tumor suppressive and oncogenic roles in gastric cancer

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3585 ◽  
Author(s):  
Tianfang Wang ◽  
Yining Liu ◽  
Min Zhao
Keyword(s):  
Gastric Cancer ◽  
Cancer Progression ◽  
Complex Disease ◽  
Mutational Analysis ◽  
Driver Mutations ◽  
Driver Genes ◽  
Protein Coding ◽  
Mirna Genes ◽  
Genetic Mechanisms ◽  
New Treatment

Gastric cancer (GC) is a complex disease with heterogeneous genetic mechanisms. Genomic mutational profiling of gastric cancer not only expands our knowledge about cancer progression at a fundamental genetic level, but also could provide guidance on new treatment decisions, currently based on tumor histology. The fact that precise medicine-based treatment is successful in a subset of tumors indicates the need for better identification of clinically related molecular tumor phenotypes, especially with regard to those driver mutations on tumor suppressor genes (TSGs) and oncogenes (ONGs). We surveyed 313 TSGs and 160 ONGs associated with 48 protein coding and 19 miRNA genes with both TSG and ONG roles. Using public cancer mutational profiles, we confirmed the dual roles of CDKN1A and CDKN1B. In addition to the widely recognized alterations, we identified another 82 frequently mutated genes in public gastric cancer cohort. In summary, these driver mutation profiles of individual GC will form the basis of personalized treatment of gastric cancer, leading to substantial therapeutic improvements.

Incidental capture of sea-snakes (Hydrophiidae) by prawn trawlers in the Gulf of Carpentaria, Australia

1994 ◽  
Vol 45 (3) ◽  
pp. 429 ◽  
Author(s):  
TJ Wassenberg ◽  
JP Salini ◽  
H Heatwole ◽  
JD Kerr
Keyword(s):  
Survival Rate ◽  
Coastal Waters ◽  
Significant Interaction ◽  
Catch Per Unit Effort ◽  
Sea Snake ◽  
Incidental Capture ◽  
Seasonal Movement ◽  
Sea Snakes ◽  
Breeding Cycles ◽  
Shallow Coastal Waters

Sea-snakes were collected from research trawlers and commercial prawn trawlers in the Gulf of Carpentaria during the period from April 1976 to December 1991. The data were analysed on the basis of CPUE (catch per unit effort) for depth, latitude and season. The research trawlers, operating in the eastern Gulf of Carpentaria, and the commercial prawn trawlers, operating in the south-western Gulf of Carpentaria, caught sea-snakes at a rate of 0.028 and 0.026 sea-snakes per metre of headrope length per hour, respectively. Lapemis hardwickii was the sea-snake most commonly caught by the research trawlers-53% of all snakes-and Hydrophis elegans was the sea-snake most commonly caught by commercial trawlers-25% of all snakes. Depth was the most significant factor affecting CPUE, with more than 70% of all sea-snakes being caught in waters less than 15 m deep. When catches of all species were combined, a significant interaction (P<0.05) existed between depth and season. L. hardwickii specimens were caught more frequently in shallow coastal waters (< 15 m deep) in spring but in deeper water further offshore in autumn. A significant interaction between latitude and depth was found for Astrotia stokesii; specimens were caught more frequently in deeper water at 14% Enhydrina schistosa is generally coastal, with 8800 of specimens being caught in water less than 10 m deep. Seasonal movement of sea-snakes between inshore and offshore waters may be linked to their breeding cycles. The estimated number of sea-snakes captured in the Gulf of Carpentaria for the 1991 prawning season ranged from 73 583 to 165 559, with a mean of 119 571. The survival rate of sea-snakes from commercial prawn trawls was about 60% and hence between 29 801 and 67 051 sea-snakes are estimated to have died.

Hydrophis donaldi (Elapidae, Hydrophiinae), a highly distinctive new species of sea snake from northern Australia

Zootaxa ◽  
2012 ◽  
Vol 3201 (1) ◽  
pp. 45 ◽  
Author(s):  
KANISHKA D.B. UKUWELA ◽  
KATE L. SANDERS ◽  
BRYAN G. FRY
Keyword(s):  
New Species ◽  
Habitat Preferences ◽  
The Body ◽  
Colour Pattern ◽  
Northern Australia ◽  
Nucleotide Substitutions ◽  
Sea Snake ◽  
Sea Snakes ◽  
Morphological Diagnosis ◽  
By Catch

A new species of viviparous sea snake, Hydrophis donaldi sp. nov. (Hydrophiinae), is described from the Gulf of Carpen-taria, northern Australia. Molecular analyses reveal this species as a deeply divergent lineage within the Hydrophis sub-group, and separate it from all other sampled taxa by fixed nucleotide substitutions at three independent mitochondrial andnuclear loci. The new species is assigned to Hydrophis based on the current morphological diagnosis of this large but pa-raphyletic genus, and is distinguished from all other Hydrophis species and closely allied genera by a combination of mor-phological characters relating to scalation, colour pattern and osteology. Using current keys for sea snakes, H. donaldi sp.nov. might be mistaken for H. coggeri, H. sibauensis or H. torquatus diadema but it is readily distinguished from thesespecies by a higher number of bands on the body and tail, lower ventral count, strongly spinous body scales, and a wider,more rounded head. Sea snakes have been sampled intensively in the Gulf of Carpentaria due to their vulnerability to by-catch in the region’s commercial prawn-trawl fisheries. That this highly distinctive new species has evaded discovery inthe region until now is surprising, but might be explained by its habitat preferences. All known specimens of H. donaldi sp. nov. were found in estuarine habitats that are relatively poorly surveyed and are not targeted by commercial fisheries.

scholarly journals Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 535 ◽  
Author(s):  
Leslie Barclay ◽  
Jennifer L. Cannon ◽  
Mary E. Wikswo ◽  
Annie R. Phillips ◽  
Hannah Browne ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Case ◽  
Molecular Data ◽  
Antigenic Drift ◽  
The Novel ◽  
Structural Protein ◽  
Protein Coding ◽  
Recombinant Viruses ◽  
The Us ◽  
Genomic Regions

Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation.

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