23 results on '"Yunyun Lv"'
Search Results
2. The American Paddlefish Genome Provides Novel Insights into Chromosomal Evolution and Bone Mineralization in Early Vertebrates
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Peilin Cheng, Kai Han, Qiong Shi, Chao Bian, Huan Ye, Qiwei Wei, Yunyun Lv, Rui Ruan, Yanping Li, Hui Zhang, Yu Huang, Chengyou Wang, Chuangju Li, Junming Xu, Chengcheng Shi, Zhiqiang Ruan, Xinxin You, Hao Du, and Jinming Wu
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Acipenseriformes ,chromosome evolution ,AcademicSubjects/SCI01180 ,Genome ,Chromosomes ,American paddlefish ,Calcification, Physiologic ,early vertebrates ,Polyploid ,Gene duplication ,Genetics ,Paddlefish ,Animals ,Molecular Biology ,Discoveries ,Ecology, Evolution, Behavior and Systematics ,biology ,Calcium-Binding Proteins ,Fishes ,Genes, Homeobox ,AcademicSubjects/SCI01130 ,Chromosome ,sturgeon and paddlefish ,Phosphoproteins ,biology.organism_classification ,Biological Evolution ,Chondrichthyes ,bone mineralization ,Evolutionary biology ,whole-genome duplication - Abstract
Sturgeons and paddlefishes (Acipenseriformes) occupy the basal position of ray-finned fishes, although they have cartilaginous skeletons as in Chondrichthyes. This evolutionary status and their morphological specializations make them a research focus, but their complex genomes (polyploidy and the presence of microchromosomes) bring obstacles and challenges to molecular studies. Here, we generated the first high-quality genome assembly of the American paddlefish (Polyodon spathula) at a chromosome level. Comparative genomic analyses revealed a recent species-specific whole-genome duplication event, and extensive chromosomal changes, including head-to-head fusions of pairs of intact, large ancestral chromosomes within the paddlefish. We also provide an overview of the paddlefish SCPP (secretory calcium-binding phosphoprotein) repertoire that is responsible for tissue mineralization, demonstrating that the earliest flourishing of SCPP members occurred at least before the split between Acipenseriformes and teleosts. In summary, this genome assembly provides a genetic resource for understanding chromosomal evolution in polyploid nonteleost fishes and bone mineralization in early vertebrates.
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- 2020
3. Diurnal rhythm expression of transcription factor NF-κB subunit p65 in Pelteobagrus vachellii
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Chuanjie Qin, Hu Peng, Jun Wan, Yang He, Wang Juanjuan, Qinchao Shi, and Yunyun Lv
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Fish Proteins ,0301 basic medicine ,Untranslated region ,DNA, Complementary ,Protein subunit ,Aquatic Science ,Transcription Initiation Factor IIA ,Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Complementary DNA ,Animals ,Environmental Chemistry ,Cloning, Molecular ,Transcription factor ,Catfishes ,Transcription Factor RelA ,NF-κB ,04 agricultural and veterinary sciences ,General Medicine ,Molecular biology ,Immunity, Innate ,Circadian Rhythm ,Open reading frame ,030104 developmental biology ,Gene Expression Regulation ,chemistry ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Gram-Negative Bacterial Infections ,Nuclear localization sequence - Abstract
The pleiotropic transcription factor nuclear factor-kappa B (NF-κB) has important functions in viral resistance. In the present study, we isolated a p65 subunit of NF-κB cDNA from Pelteobagrus vachellii (termed Pvp65) and characterized it. The full-length p65 cDNA comprised 3651 bp, including a 148-bp 5'-untranslated region (UTR), a 106-bp 3'-UTR, and an open reading frame encoding a 1067-amino acid putative protein. The protein sequence comprised a DNA binding motif, a Rel-homology domain, a Rel protein signature, a putative transcription activation domain, a nuclear localization signal, and a transcription initiation factor IIA domain. The expression of Pvp65 displayed a daily rhythm, with an acrophase at approximately at 15:32 h in the liver, 11:34 h in the spleen, and 16:45 h in the head kidney. In addition, infection with Aeromonas hydrophila caused Pvp65 expression to increase significantly (P 0.05), and peaking at 12 h post infection in the spleen, at 24 in the head kidney, and at 12 h in the liver. Thus, NF-κB expression might be under light/dark cycle control in P. vachellii, and may be involved in the immune response to A. hydrophila.
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- 2020
4. Discovery of differentially expressed genes in the intestines of Pelteobagrus vachellii within a light/dark cycle
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He Yang, Chuanjie Qin, Wang Jun, Sun Jiaxian, Yongwang Han, Hu Peng, Shi Qingchao, and Yunyun Lv
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Genetics ,Schedule ,Physiology ,Photoperiod ,Dark cycle ,030209 endocrinology & metabolism ,Biology ,Circadian Rhythm ,Intestines ,03 medical and health sciences ,0302 clinical medicine ,Differentially expressed genes ,Physiology (medical) ,Animals ,Circadian rhythm ,Transcriptome ,Pelteobagrus vachellii ,Catfishes ,030217 neurology & neurosurgery - Abstract
In aquaculture, it is necessary to determine of the diurnal biological variations in the intestines to determine an appropriate feeding schedule. The present study aimed to examine the transcriptomes of the
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- 2019
5. Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli
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Jinlong Yang, Qiong Shi, Yanping Li, Xiaoai Wang, Yuanwei Zhang, Chao Sun, Jia Li, Xiao-Fu Pan, Jun-Xing Yang, Xinxin You, Xinhui Zhang, Yunyun Lv, Wansheng Jiang, Le Cheng, Chao Bian, Shuwei Liu, and Kunfeng Yang
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Fish Proteins ,Bagarius ,Sequence assembly ,Biology ,flesh color ,Genome ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Bagarius yarrelli ,Genetics ,Animals ,Catfishes ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Whole Genome Sequencing ,Contig ,giant devil catfish ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Genomics ,biology.organism_classification ,Genome Report ,Gene Expression Regulation ,whole-genome sequencing ,Evolutionary biology ,Ictalurus ,genome assembly ,Transcriptome ,body size ,030217 neurology & neurosurgery ,Catfish - Abstract
As one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10–30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in fish muscles, and also potential organisms for extensive utilization in Asian freshwater aquaculture. In a combination of Illumina and PacBio sequencing technologies, we de novo assembled a 571-Mb genome for the giant devil catfish from a total of 153.4-Gb clean reads. The scaffold and contig N50 values are 3.1 and 1.6 Mb, respectively. This genome assembly was evaluated with 93.4% of Benchmarking Universal Single-Copy Orthologs completeness, 98% of transcripts coverage, and highly homologous with a chromosome-level-based genome of channel catfish (Ictalurus punctatus). We detected that 35.26% of the genome assembly is composed of repetitive elements. Employing homology, de novo, and transcriptome-based annotations, we annotated a total of 19,027 protein-coding genes for further use. In summary, we generated the first high-quality genome assembly of the giant devil catfish, which provides an important genomic resource for its future studies such as the body size and flesh color issues, and also for facilitating the conservation and utilization of this valuable catfish.
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- 2019
6. High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database
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Jieming Chen, Yu Huang, Yunyun Lv, Junmin Xu, Yunhai Yi, Chao Bian, Qiong Shi, Li Deng, and Xinxin You
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Fish Proteins ,Gills ,0106 biological sciences ,High-throughput screening ,Antimicrobial peptides ,Computational biology ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Immune system ,Databases, Genetic ,Genetics ,Animals ,030304 developmental biology ,0303 health sciences ,Innate immune system ,biology ,Fishes ,Actinopterygii ,Genetic Variation ,biology.organism_classification ,Drug development ,Genetic marker ,Antimicrobial Cationic Peptides ,010606 plant biology & botany - Abstract
Analyses of transcriptomic datasets have the potential to reveal genetic markers underlying ecological adaptations. In the present study, we leverage the expanding dataset generated by the Fish-T1K Project (Transcriptomes of 1000 Fishes) to characterize small peptides that may be implicated in the immune system of fishes. We focused our analyses on sequences smaller than 360 bp obtained from gill transcriptomes of 87 ray-finned fishes (Actinopterygii). Functional annotation of short transcripts revealed that the number of small immune peptides varied significantly among the studied species. High-throughput screening of antimicrobial peptides (AMPs) with homologous searches was used to characterize the composition of innate immune defense factors present in fishes. We analyzed the putative effects of habitat, climatic zone and genetic system on the distribution of small peptides among species. Our results highlight the utility of large transcriptomic datasets such as Fish-T1K to explore patterns of variation at macroevolutionary scales and to discover novel peptides that may be used for further investigation and drug development.
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- 2019
7. The structural and functional divergence of a neglected three-finger toxin subfamily in lethal elapids
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Zhi-Yi, Zhang, Yunyun, Lv, Wei, Wu, Chaochao, Yan, Chen-Yang, Tang, Changjun, Peng, and Jia-Tang, Li
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Elapid Venoms ,Bungarus ,Antivenins ,Animals ,Elapidae ,Three Finger Toxins ,General Biochemistry, Genetics and Molecular Biology - Abstract
Bungarus multicinctus is a widely distributed and medically important elapid snake that produces lethal neurotoxic venom. To study and enhance existing antivenom, we explore the complete repertoire of its toxin genes based on de novo chromosome-level assembly and multi-tissue transcriptome data. Comparative genomic analyses suggest that the three-finger toxin family (3FTX) may evolve through the neofunctionalization of flanking LY6E. A long-neglected 3FTX subfamily (i.e., MKA-3FTX) is also investigated. Only one MKA-3FTX gene, which evolves a different protein conformation, is under positive selection and actively transcribed in the venom gland, functioning as a major toxin effector together with MKT-3FTX subfamily homologs. Furthermore, this lethal snake may acquire self-resistance to its β-bungarotoxin via amino acid replacements on fast-evolving KCNA2. This study provides valuable resources for further evolutionary and structure-function studies of snake toxins, which are fundamental for the development of effective antivenoms and drug candidates.
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- 2022
8. The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders
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Shengtao Guo, Fan Li, Yunyun Lv, Daiqin Li, Qiong Shi, Chao Bian, Zhengyong Wen, and Xinhui Zhang
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0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Evolution ,Silk ,Biology ,010603 evolutionary biology ,01 natural sciences ,Desis jiaxiangi ,03 medical and health sciences ,Phylogenetics ,Evolution of spiders ,QH359-425 ,Animals ,QH540-549.5 ,Phylogeny ,Spider ,Ecology ,Base Sequence ,Phylogenetic tree ,Intertidal spider ,Spiders ,General Medicine ,biology.organism_classification ,Argyroneta aquatica ,Positive selection ,Mitogenome ,030104 developmental biology ,Evolutionary biology ,Hypochilus thorelli ,Genome, Mitochondrial ,Diving bell spider ,Research Article - Abstract
Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.
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- 2021
9. Morphometric and population genomic evidence for species divergence in the Chimarrichthys fish complex of the Tibetan Plateau
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Yunyun Lv, Yanping Li, Zuogang Peng, and Christopher P. Burridge
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0106 biological sciences ,0301 basic medicine ,Gene Flow ,Range (biology) ,Genetic Speciation ,Climate ,Population ,Single-nucleotide polymorphism ,Biology ,Tibet ,010603 evolutionary biology ,01 natural sciences ,Polymorphism, Single Nucleotide ,Population genomics ,03 medical and health sciences ,Rivers ,Genetics ,Animals ,education ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Catfishes ,Phylogeny ,Morphometrics ,geography ,education.field_of_study ,Plateau ,geography.geographical_feature_category ,Genome ,Altitude ,030104 developmental biology ,Genetics, Population ,Evolutionary biology ,Genetic structure ,Metagenomics - Abstract
The uplift of the Tibetan Plateau altered the environmental conditions of the local area substantially. Here, we conducted a comprehensive investigation based on morphometrics, population genomics, and climatic factors to evaluate phenotypic and genome-level variations in a radiation of Chimarrichthys catfish endemic to the Plateau. Discriminant function analysis showed phenotypic differences of Chimarrichthys between rivers with respect to elevation. Genetic structure analysis based on 6606 single nucleotide polymorphisms (SNPs) deduced genetic differences between rivers, and species delimitation indicated that the Chimarrichthys fish complex could be divided into three species. Restriction site-associated DNA tags were mapped to the gene sets of Glyptosternon maculatum, and matches were searched against databases for Gene Ontology annotation. Genomic regions exhibiting marked differences among localities represented a range of biological functions, including growth (gdf11), bone development (bmp8a), cellular response to light stimulus (opn3), regulation of the rhodopsin-mediated signalling pathway (grk1), immune response (rag1 and ung), reproductive process (antxr2), and regulation of intracellular iron levels (ireb2). The tag44126, where gene gdf11 is located, was identified as an outlier exhibiting divergence between rivers with altitude differences, and the SNP is thymine (T) in Dadu and Yalong River (~2700 m), but guanine (G) in Jinsha and Qingyi rivers (~2200 and ~ 684 m), suggesting a possible effect of altitude on its differentiation.
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- 2020
10. Genome and Transcriptome Sequencing of
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Chao, Bian, Weiting, Chen, Zhiqiang, Ruan, Zhe, Hu, Yu, Huang, Yunyun, Lv, Tengfei, Xu, Jia, Li, Qiong, Shi, and Wei, Ge
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Male ,Genome ,casper ,Pigmentation ,Chromosome Mapping ,Zebrafish Proteins ,transcriptome sequencing ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,Article ,genome sequencing ,iridophore degeneration ,Mutation ,roy ,Animals ,Female ,variation ,Transcriptome ,Zebrafish - Abstract
casper has been a widely used transparent mutant of zebrafish. It possesses a combined loss of reflective iridophores and light-absorbing melanophores, which gives rise to its almost transparent trunk throughout larval and adult stages. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. To identify the potential genetic basis of this fascinating morphological phenotype, we constructed genome maps by performing genome sequencing of 28 zebrafish individuals including wild-type AB strain, roy orbison (roy), and casper mutants. A total of 4.3 million high-quality and high-confidence homozygous single nucleotide polymorphisms (SNPs) were detected in the present study. We also identified a 6.0-Mb linkage disequilibrium block specifically in both roy and casper that was composed of 39 functional genes, of which the mpv17 gene was potentially involved in the regulation of iridophore formation and maintenance. This is the first report of high-confidence genomic mutations in the mpv17 gene of roy and casper that potentially leads to defective splicing as one major molecular clue for the iridophore loss. Additionally, comparative transcriptomic analyses of skin tissues from the AB, roy and casper groups revealed detailed transcriptional changes of several core genes that may be involved in melanophore and iridophore degeneration. In summary, our updated genome and transcriptome sequencing of the casper and roy mutants provides novel genetic clues for the iridophore loss. These new genomic variation maps will offer a solid genetic basis for expanding the zebrafish mutant database and in-depth investigation into pigmentation of animals.
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- 2020
11. Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation
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Qiong Shi, Ruobo Gu, Di-An Fang, Zhijuan Nie, Xinxin You, Junmin Xu, Li Quanjie, Wei Ge, Tao Jiang, Dongpo Xu, Pao Xu, Yanbing Zhuang, Gao Jiancao, Nailin Shao, Kai Liu, Wang Yuyu, Yu Huang, Hongbo Liu, Yunyun Lv, Chao Bian, Gangchun Xu, Jia Li, Jian Yang, and Hongxia Li
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Fish Proteins ,0106 biological sciences ,Candidate gene ,Population ,Adaptation, Biological ,Population genetics ,Sequence assembly ,Health Informatics ,010603 evolutionary biology ,01 natural sciences ,Genome ,Chromosomes ,03 medical and health sciences ,Anchovy ,Animals ,RNA, Messenger ,education ,genome and population sequencing ,migratory dimorphism and adaptation ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Coilia nasus ,Whole Genome Sequencing ,biology ,Research ,Gene Expression Profiling ,Fishes ,Computational Biology ,Genetic Variation ,Molecular Sequence Annotation ,biology.organism_classification ,Computer Science Applications ,Gene Ontology ,Genetics, Population ,Gene Expression Regulation ,Evolutionary biology ,genome assembly ,Animal Migration ,Calcium ,Seasons ,Adaptation ,Chinese tapertail anchovy (Coilia nasus) - Abstract
Background Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). Results In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. Conclusions We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.
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- 2020
12. A comprehensive phylogeny of the genus Kurixalus (Rhacophoridae, Anura) sheds light on the geographical range evolution of frilled swamp treefrogs
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Yunyun Lv, Jia-Tang Li, Rafe M. Brown, Kai He, and Sebastian Klaus
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0106 biological sciences ,0301 basic medicine ,Asia ,Time Factors ,Range (biology) ,Biogeography ,Holocene climatic optimum ,DNA, Mitochondrial ,010603 evolutionary biology ,01 natural sciences ,Swamp ,03 medical and health sciences ,Genetics ,Animals ,East Asia ,14. Life underwater ,Molecular Biology ,Kurixalus ,Rhacophoridae ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,geography ,geography.geographical_feature_category ,Base Sequence ,Geography ,biology ,Fossils ,Ecology ,Bayes Theorem ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,13. Climate action ,Wetlands ,Biological dispersal ,Anura - Abstract
Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group is ideal for the study of terrestrial range evolution, especially that portion of its range that extends into the island archipelagos of Southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations. A variety of ancestral-area reconstruction strategies were employed to estimate past changes of the species’ geographical range, and to evaluate the impact of different abiotic barriers on range evolution. We found that frilled swamp treefrogs probably originated in Taiwan or South Vietnam in the Oligocene. Alternatively, the lineage leading to Kurixalus appendiculatus strongly supports a hypothesis of terrestrial connection between the Indian and Asian continents in the Oligocene. The outcome of both our divergence-time estimates and ancestral-area reconstruction suggests that the divergence between species from Indochina and Taiwan can probably be attributed to the opening of the South China Sea, approximately 33 million years ago. We could not find evidence for dispersal between mainland China and Taiwan Island. Formation of both Mekong and Red River valleys did not have any impact on Kurixalus species diversification. However, coincidence in timing of climate change and availability of plausible dispersal routes from the Oligocene to the middle Miocene, plausibly implied that Kurixalus diversification in Asia resulted from contemporaneous, climate-induced environmental upheaval (Late Oligocene Warming at 29 Ma; Mi-1 glaciation since 24.4–21.5 Ma; Mid-Miocene Climatic Optimum at 14 Ma), which alternatively opened and closed dispersal routes.
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- 2018
13. Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq
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Yunyun Lv, Chao Bian, Feng Zhao, Qiong Shi, Kai Zhang, Jianan Xu, Dongpo Xu, Jian Liu, Xinxin You, Gangchun Xu, Min Wang, Jianhui Wu, Zheng Yueping, Ping Zhuang, Kai Liu, Fan Houyong, Junmin Xu, Chen Jinhui, Zhiqiang Ruan, and Pao Xu
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0301 basic medicine ,China ,Population ,Zoology ,Biology ,Acipenser sinensis ,DNA, Mitochondrial ,Polymorphism, Single Nucleotide ,General Biochemistry, Genetics and Molecular Biology ,Nucleotide diversity ,03 medical and health sciences ,Sturgeon ,Rivers ,Effective population size ,Animals ,Genetic variability ,education ,General Environmental Science ,education.field_of_study ,Genetic diversity ,Genome ,Endangered Species ,Fishes ,Genetic Variation ,Sequence Analysis, DNA ,biology.organism_classification ,Mitochondria ,Genetics, Population ,030104 developmental biology ,Haplotypes ,Genetic structure ,Female ,General Agricultural and Biological Sciences - Abstract
As a living fossil, the endangered Chinese sturgeon ( Acipenser sinensis ) has been considered a national treasure in China. Here, the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes. The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths (10–35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA (mtDNA) D-loop region and 1,481,620 SNPs (single-nucleotide polymorphisms) generated by restriction site-associated DNA sequencing (RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.
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- 2018
14. Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes
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Shaosen Yang, Chao Bian, Weiwei Chen, Xinxin You, Xueqiang Lin, Yunyun Lv, Ruobo Gu, Junmin Xu, Xinhui Zhang, Zhengyong Wen, Lizhen Ye, Jia Li, and Qiong Shi
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0106 biological sciences ,Pharmaceutical Science ,Japanese eel (Anguilla japonica) ,01 natural sciences ,Genome ,Japan ,Drug Discovery ,Gene cluster ,Japanese eel ,Tetraodontidae ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,Zebrafish ,lcsh:QH301-705.5 ,Phylogeny ,0303 health sciences ,biology ,pelvic fin ,Ocean sunfish ,Genomics ,Multigene Family ,Animal Fins ,Female ,tbx4 ,Fish Proteins ,fin spine ,animal structures ,tbx4 gene cluster ,010603 evolutionary biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,Animals ,genome sequencing and assembly ,Gene ,030304 developmental biology ,teleost fish ,Whole Genome Sequencing ,Molecular Sequence Annotation ,Gnathostomata ,Anguilla ,biology.organism_classification ,lcsh:Biology (General) ,Evolutionary biology ,Mutation ,T-Box Domain Proteins ,Sequence Alignment - Abstract
Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.
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- 2019
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15. Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias
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Yunyun Lv, Qiong Shi, Jia Li, Xiyang Chen, Yunhai Yi, Chao Bian, Xinxin You, Xueqiang Lin, and Yiping Zhang
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Fish Proteins ,food.ingredient ,genome annotation ,antimicrobial peptide ,Pharmaceutical Science ,Zoology ,blue tilapia (Oreochromis aureus) ,Aquaculture ,Genome ,Article ,03 medical and health sciences ,Nile tilapia ,food ,Drug Discovery ,Animals ,Oreochromis aureus ,lcsh:QH301-705.5 ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,030304 developmental biology ,Molecular breeding ,Whole genome sequencing ,0303 health sciences ,whole genome sequencing ,biology ,business.industry ,Tilapia ,Cichlids ,04 agricultural and veterinary sciences ,Genome project ,biology.organism_classification ,lcsh:Biology (General) ,040102 fisheries ,genome assembly ,Hybridization, Genetic ,0401 agriculture, forestry, and fisheries ,Female ,business ,human activities ,Antimicrobial Cationic Peptides - Abstract
Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.
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- 2019
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16. Whole Genome Sequencing of Chinese White Dolphin (
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Kuntong, Jia, Chao, Bian, Yunhai, Yi, Yanping, Li, Peng, Jia, Duan, Gui, Xiyang, Zhang, Wenzhi, Lin, Xian, Sun, Yunyun, Lv, Jia, Li, Xinxin, You, Qiong, Shi, Meisheng, Yi, and Yuping, Wu
- Subjects
Biological Products ,China ,whole genome sequencing ,Dolphins ,Endangered Species ,Adaptation, Biological ,Molecular Sequence Annotation ,antihypertensive peptide ,Article ,High-Throughput Screening Assays ,Drug Development ,Hypertension ,genome assembly ,Animals ,Humans ,Chinese white dolphin (Sousa chinensis) ,Peptides ,Antihypertensive Agents - Abstract
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.
- Published
- 2019
17. The First Transcriptome Assembly of Yenyuan Stream Salamander (Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution
- Author
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Yunyun Lv, Yong Huang, Qiangqiang Liu, and Jianli Xiong
- Subjects
0106 biological sciences ,0301 basic medicine ,China ,Time Factors ,Lineage (evolution) ,Urodela ,Chinese giant salamander ,Batrachuperus ,010603 evolutionary biology ,01 natural sciences ,Catalysis ,Article ,Inorganic Chemistry ,Evolution, Molecular ,lcsh:Chemistry ,03 medical and health sciences ,Rivers ,Species Specificity ,Phylogenetics ,biology.animal ,Animals ,Physical and Theoretical Chemistry ,Molecular Biology ,lcsh:QH301-705.5 ,Spectroscopy ,Phylogeny ,biology ,Phylogenetic tree ,Geography ,Organic Chemistry ,General Medicine ,biology.organism_classification ,salamander ,Computer Science Applications ,Yenyuan stream salamander ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Evolutionary biology ,Multigene Family ,regeneration ,Salamander ,transcriptome ,divergence ,Reference genome - Abstract
The Yenyuan stream salamander (Batrachuperus yenyuanensis) has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the Scribble gene&mdash, whose function is related to regeneration&mdash, based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander (Andrias davidianus) of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.
- Published
- 2019
18. Molecular evolution of melatonin receptor genes (mtnr) in vertebrates and its shedding light on mtnr1c
- Author
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Yunyun Lv, Qiong Shi, Yanping Li, Chao Bian, and Xinxin You
- Subjects
0301 basic medicine ,Sequence Homology, Amino Acid ,biology ,Receptors, Melatonin ,Genomics ,General Medicine ,biology.organism_classification ,Melatonin receptor ,Genome ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Proteoglycan 4 ,Evolutionary biology ,Molecular evolution ,030220 oncology & carcinogenesis ,Vertebrates ,Gene duplication ,Genetics ,biology.protein ,Animals ,Amino Acid Sequence ,Gene ,Zebrafish - Abstract
Melatonin receptors (MTNRs) play important roles in regulation of circadian rhythms and seasonal reproduction. However, their origin and evolution in vertebrates have not been investigated. Here, we performed a comprehensive examination by comparative genome mining of MTNRs in vertebrates. We successfully extracted 164 putative encoding sequences for MTNRs (including 57 mtnr1a, 59 mtnr1b and 48 mtnr1c) from 45 high-quality representative genomes. Interestingly, the putative expansions of mtnr1a and mtnr1b in zebrafish were also identified in other Cyprinifomes, but not in other orders of teleost. Using phylogenetic interference, we observed this expansion to be clustered into a primitive position of the Actinopterygii, which may be resulted from teleost-specific genome duplication. The C-terminal extension of MTNR1C, predicted to be proteoglycan 4 (PRG4), originated after the speciation of Monotremata or Marsupialia. Our present genomics survey provides novel insights into the evolution of MTNRs in vertebrates and updates our understanding of these proteins.
- Published
- 2021
19. High Throughput Identification of Antihypertensive Peptides from Fish Proteome Datasets
- Author
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Jian Yang, Qiong Shi, Lijun Zhang, Yunhai Yi, and Yunyun Lv
- Subjects
0301 basic medicine ,collagen ,Fish Proteins ,hypertension ,Proteome ,Protein Hydrolysates ,Protein subunit ,Salmo salar ,Pharmaceutical Science ,antihypertensive peptide ,Angiotensin-Converting Enzyme Inhibitors ,Computational biology ,Article ,03 medical and health sciences ,Phylogenetics ,Drug Discovery ,Animals ,Salmo ,Receptor ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,lcsh:QH301-705.5 ,Antihypertensive Agents ,Phylogeny ,chemistry.chemical_classification ,030109 nutrition & dietetics ,biology ,high throughput identification ,Fishes ,biology.organism_classification ,030104 developmental biology ,Enzyme ,chemistry ,lcsh:Biology (General) ,Seafood ,fish protein hydrolysate ,Identification (biology) ,Peptides - Abstract
Antihypertensive peptides (AHTPs) are a group of small peptides with the main role to block key enzymes or receptors in the angiotensin genesis pathway. A great number of AHTPs have been isolated or digested from natural food resources, however, comprehensive studies on comparisons of AHTPs in various species from the perspective of big data are rare. Here, we established a simplified local AHTP database, and performed in situ mapping for high throughput identification of AHTPs with high antihypertensive activity from high-quality whole proteome datasets of 18 fish species. In the 35 identified AHTPs with reported high activity, we observed that Gly-Leu-Pro, Leu-Pro-Gly, and Val-Ser-Val are the major components of fish proteins, and AHTP hit numbers in various species demonstrated a similar distributing pattern. Interestingly, Atlantic salmon (Salmo salar) is in possession of far more abundant AHTPs compared with other fish species. In addition, collagen subunit protein is the largest group with more matching AHTPs. Further exploration of two collagen subunits (col4a5 and col8a1) in more fish species suggested that the hit pattern of these conserved proteins among teleost is almost the same, and their phylogeny is consistent with the evolution of these fish species. In summary, our present study provides basic information for the relationship of AHTPs with fish proteins, which sheds light on rapid discovery of marine drugs or food additives from fish protein hydrolysates to alleviate hypertension.
- Published
- 2018
20. A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates
- Author
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Yanping Li, Xinxin You, Yunyun Lv, Chao Bian, Qiong Shi, and Li Deng
- Subjects
0301 basic medicine ,Nonsynonymous substitution ,Pseudogene ,pseudogene ,Pharmaceutical Science ,Synteny ,l-aromatic amino acid decarboxylase (AAAD) ,Article ,Analytical Chemistry ,Amphibians ,Birds ,Evolution, Molecular ,lcsh:QD241-441 ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Organic chemistry ,Molecular evolution ,biology.animal ,vertebrate ,Drug Discovery ,l<%2Fspan>-aromatic+amino+acid+decarboxylase+%28AAAD%29%22">l-aromatic amino acid decarboxylase (AAAD) ,melatonin biosynthesis ,molecular evolution ,Animals ,Physical and Theoretical Chemistry ,Gene ,Phylogeny ,Mammals ,Genome ,Phylogenetic tree ,biology ,Organic Chemistry ,Fishes ,Vertebrate ,Reptiles ,Stop codon ,030104 developmental biology ,Chemistry (miscellaneous) ,Evolutionary biology ,Aromatic-L-Amino-Acid Decarboxylases ,Vertebrates ,Molecular Medicine ,030217 neurology & neurosurgery ,Pseudogenes - Abstract
Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad-like gene, which formed a novel AAAD family. However, in tetraploid teleosts, there were two copies of the aaad gene due to whole genome duplication. A subsequent synteny analysis investigated 81 aaad sequences and revealed their collinearity and systematic evolution. Interestingly, we discovered that platypus (Ornithorhynchus anatinus), Atlantic cod (Guadus morhua), Mexican tetra (Astyanax mexicanus), and a Sinocyclocheilus cavefish (S. anshuiensis) have long evolutionary branches in the phylogenetic topology. We also performed pseudogene identification and selection pressure analysis; however, the results revealed a deletion of 37 amino acids in Atlantic cod and premature stop codons in the cave-restricted S. anshuiensis and A. mexicanus, suggesting weakening or disappearing rhythms in these cavefishes. Selective pressure analysis of aaad between platypus and other tetrapods showed that rates of nonsynonymous (Ka) and synonymous (Ks) substitutions were higher when comparing the platypus to other representative tetrapods, indicating that, in this semiaquatic mammal, the aaad gene experienced selection during the process of evolution. In summary, our current work provides novel insights into aaad genes in vertebrates from a genome-wide view.
- Published
- 2018
21. A Genomic Survey of SCPP Family Genes in Fishes Provides Novel Insights into the Evolution of Fish Scales
- Author
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Yu Huang, Qiong Shi, Yunyun Lv, Yanping Li, Chao Bian, Jia Li, Kazuhiko Kawasaki, and Xinxin You
- Subjects
0301 basic medicine ,Fish Proteins ,Candidate gene ,Carps ,Animal Scales ,SCPP gene ,Cavefish ,Biology ,Genome ,Catalysis ,Article ,lcsh:Chemistry ,Inorganic Chemistry ,scale ,Evolution, Molecular ,03 medical and health sciences ,Gene cluster ,evolution ,Animals ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,Molecular Biology ,Gene ,Spectroscopy ,Coevolution ,Phylogeny ,Genetics ,Phylogenetic tree ,Organic Chemistry ,Calcium-Binding Proteins ,General Medicine ,Phosphoproteins ,Phenotype ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,cavefish ,Multigene Family ,mutation - Abstract
The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi. According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes. In addition, most of these SCPP genes, with the exception of SPP1, individually form one or two gene cluster(s) on each corresponding genome. Furthermore, we constructed phylogenetic trees using maximum likelihood method to estimate their evolution. The phylogenetic topology mostly supports two subclasses in some species, such as Cyprinus carpio, Sinocyclocheilus anshuiensis, S. grahamin, and S. rhinocerous, but not in the other examined fishes. By comparing the gene structures of recently reported candidate genes, SCPP1 and SCPP5, for determining scale phenotypes, we found that the hypothesis is suitable for Astyanax mexicanus, but denied by S. anshuiensis, even though they are both sparsely scaled for cave adaptation. Thus, we conclude that, although different fish species display similar scale phenotypes, the underlying genetic changes however might be diverse. In summary, this paper accelerates the recognition of the SCPP family in teleosts for potential scale evolution.
- Published
- 2017
22. DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)
- Author
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Ning-Xin Dang, Yunyun Lv, Robert W. Murphy, Bo-Han Zhao, Jia-Tang Li, Feng-Hui Sun, Wen-Zhi Wang, and Jichao Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Species complex ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,Electron Transport Complex IV ,03 medical and health sciences ,Genetics ,Animals ,DNA Barcoding, Taxonomic ,Molecular Biology ,Rhacophoridae ,Neighbor joining ,Kurixalus ,biology ,Phylogenetic tree ,Ecology ,Rhacophorus ,Cytochrome c oxidase subunit I ,Bayes Theorem ,Sequence Analysis, DNA ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Genome, Mitochondrial ,Anura - Abstract
The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.
- Published
- 2015
23. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey
- Author
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Daiji Endoh, Yanping Li, Xinxin You, Junmin Xu, Qiong Shi, Yunyun Lv, Chao Bian, and Hiroki Teraoka
- Subjects
0301 basic medicine ,endocrine system ,lcsh:QH426-470 ,Protein Conformation ,Xenopus ,tryptophan hydroxylase (TPH) ,Tryptophan Hydroxylase ,Article ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Molecular evolution ,positive selection ,biology.animal ,vertebrate ,Genetics ,Animals ,Humans ,Selection, Genetic ,Gene ,Zebrafish ,Genetics (clinical) ,melatonin biosynthesis ,TPH1 ,Phylogenetic tree ,biology ,TPH2 ,molecular evolution ,phylogenetic analysis ,Vertebrate ,Tryptophan hydroxylase ,Turtles ,serotonin ,lcsh:Genetics ,030104 developmental biology ,Evolutionary biology ,Chickens ,hormones, hormone substitutes, and hormone antagonists ,030217 neurology & neurosurgery ,Functional divergence - Abstract
Serotonin is a neurotransmitter involved in various physiological processes in the central and peripheral nervous systems. Serotonin is also a precursor for melatonin biosynthesis, which mainly occurs in the pineal gland of vertebrates. Tryptophan hydroxylase (TPH) acts as the rate-limiting enzyme in serotonin biosynthesis and is the initial enzyme involved in the synthesis of melatonin. Recently, two enzymes&mdash, TPH1 and TPH2&mdash, were reported to form the TPH family in vertebrates and to play divergent roles in serotonergic systems. Here, we examined the evolution of the TPH family from 70 vertebrate genomes. Based on the sequence similarity, we extracted 184 predicted tph homologs in the examined vertebrates. A phylogenetic tree, constructed on the basis of these protein sequences, indicated that tph genes could be divided into two main clades (tph1 and tph2), and that the two clades were further split into two subgroups of tetrapods and Actinopterygii. In tetrapods, and some basal non-teleost ray-finned fishes, only two tph isotypes exist. Notably, tph1 in most teleosts that had undergone the teleost-specific genome duplication could be further divided into tph1a and tph1b. Moreover, protein sequence comparisons indicated that TPH protein changes among vertebrates were concentrated at the NH2-terminal. The tertiary structures of TPH1 and TPH2 revealed obvious differences in the structural elements. Five positively selected sites were characterized in TPH2 compared with TPH1, these sites may reflect the functional divergence in enzyme activity and substrate specificity. In summary, our current work provides novel insights into the evolution of tph genes in vertebrates from a comprehensive genomic perspective.
- Published
- 2019
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