scholarly journals Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides

Marine Drugs ◽  
2019 ◽  
Vol 17 (9) ◽  
pp. 504 ◽  
Author(s):  
Kuntong Jia ◽  
Chao Bian ◽  
Yunhai Yi ◽  
Yanping Li ◽  
Peng Jia ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Bioactive Peptides ◽  
Draft Genome ◽  
Comparative Genomic ◽  
Cetacean Species ◽  
Terrestrial Mammals ◽  
Chinese White ◽  
Sousa Chinensis ◽  
Chinese White Dolphin ◽  
Antihypertensive Peptides

Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.

scholarly journals Conservation of the Eastern Taiwan Strait Chinese White Dolphin (Sousa chinensis): Fishers' Perspectives and Management Implications

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0161321 ◽  
Author(s):  
Ta-Kang Liu ◽  
Yu-Cheng Wang ◽  
Laurence Zsu-Hsin Chuang ◽  
Chih-How Chen
Keyword(s):  
Taiwan Strait ◽  
Management Implications ◽  
Chinese White ◽  
Sousa Chinensis ◽  
Chinese White Dolphin

scholarly journals Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Rose Waldron ◽  
Jamie McGowan ◽  
Natasha Gordon ◽  
Charley McCarthy ◽  
E. Bruce Mitchell ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Prediction ◽  
Draft Genome ◽  
Dermatophagoides Pteronyssinus ◽  
Mite Species ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Dust Mite ◽  
Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

scholarly journals The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

scholarly journals Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott C. Thomas ◽  
Devon Payne ◽  
Kevin O. Tamadonfar ◽  
Cale O. Seymour ◽  
Jian-Yu Jiao ◽  
...  
Keyword(s):  
United States ◽  
Amino Acids ◽  
Draft Genome ◽  
The United States ◽  
Pentose Phosphate ◽  
High Abundance ◽  
Comparative Genomic ◽  
Labeled Compounds ◽  
Geothermal Systems

Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

Chinese White Dolphin Detection in the Wild

2021 ◽  
Author(s):  
Hao Zhang ◽  
Qi Zhang ◽  
Phuong Anh Nguyen ◽  
Victor C. S. Lee ◽  
Antoni Chan
Keyword(s):  
Chinese White ◽  
In The Wild ◽  
Chinese White Dolphin

Draft genome sequence of multidrug-resistant Bradyrhizobium sp. BL isolated from a sewage treatment plant in China

2019 ◽  
Author(s):  
Peng Bao ◽  
Guo-Xiang Li ◽  
Yu-Qin He ◽  
Yi Dai
Keyword(s):  
Antibiotic Resistance ◽  
Municipal Wastewater ◽  
Draft Genome ◽  
Sewage Treatment Plant ◽  
Treatment Plant ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Municipal Wastewater Treatment ◽  
Total Size ◽  
Bradyrhizobium Sp

Abstract The genus Bradyrhizobium is considered to be widespread and abundant group of symbiotic bacteria in many plant-soil ecosystems. However, the ecological versatility of this phylogenetic group remains highly understudied in man-made ecosystems, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this genus for human health, we analyzed the high quality draft genome of Bradyrhizobium strain BL, isolated from a municipal wastewater treatment plant in Ningbo, China. The Bradyrhizobium sp. BL draft genome has a total size of 7,718,431 bp with an overall G + C content of 46.43%. From a total of 7236 predicted sequences, 7176 and 60 are protein and RNA coding sequences, respectively. Moreover, 63.51% of the predicted genes were assigned into to Clusters of Orthologous Groups (COG) functional categories. The Bradyrhizobium sp. BL genome contains various defense mechanisms against antibiotics that up to predicted 60 antibiotic resistance coding genes. The Bradyrhizobium sp. BL genome contains 237 termed virulence factors coding genes which show its potential pathogenicity. This study provides important insights into the genomic diversity of the genus Bradyrhizobium and provides a foundation for future comparative genomic studies that will generate a better understanding of the antibiotic resistance process.

scholarly journals Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

2020 ◽  
Vol 8 (5) ◽  
pp. 653 ◽  
Author(s):  
Jamie McGowan ◽  
Richard O’Hanlon ◽  
Rebecca A. Owens ◽  
David A. Fitzpatrick
Keyword(s):  
Mass Spectrometry ◽  
Plant Pathogens ◽  
Genome Structure ◽  
Draft Genome ◽  
Phytophthora Species ◽  
Comparative Genomic ◽  
Tandem Gene Duplication ◽  
Widespread Species ◽  
Forest Pathogen ◽  
Extracellular Proteome

The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species—Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.

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