Population Genetic Structure and Its Implication in the Conservation of Schizopygopsis Pylzovi in Yellow River As Inferred from Mitochondrial DNA Sequence Analysis
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Duplication of Toll-Like Receptor 22 in Teleost Fishes
Fish and Shellfish Immunology 94 (2019) 752–760 Contents lists available at ScienceDirect Fish and Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi Full length article Duplication of toll-like receptor 22 in teleost fishes T ∗ Delin Qia, , Yan Chaob, Cunfang Zhanga, Zhenji Wangc, Wei Wanga, Qichang Chena, Ziqin Zhenga,b, Zhao Zhanga,b a State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China b Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China c Fishery Environmental Monitoring Station of Qinghai Province, Xining, 810012, China ARTICLE INFO ABSTRACT Keywords: The TLRs of teleost fishes have distinct features and are highly diverse, but the duplication characteristics and Toll-like receptor 22 expression patterns of the tlr22 gene remain unclear. Here, we identified paralogous tlr22 genes in 13 teleost Duplication fishes by screening available fish genomic resources and using molecular cloning. We then conducted com- Expression pattern prehensive bioinformatics analyses and investigated spatiotemporal differences in the expression patterns of the Gymnocypris eckloni tlr22 genes in G. eckloni. The results indicated that more than three paralogous tlr22 genes were possessed by Teleost fishes some teleost fishes. Of these, tlr22c is specific to some subfamilies of the Cyprinidae (e.g., Barbinae, Cyprininae, Schizothoracinae, and Leuciscinae). Phylogenetic and syntenic analyses showed that the paralogous tlr22 genes originated from two single-gene duplication events. Molecular clock calculations dated the two gene duplication events at 49.5 and 39.3 MYA, which is before the common carp-specific genome duplication event and well after the fish-specific genome duplication. -
附录1 甘肃省鱼类种类组成appendix 1 Fish Species Composition in Gansu
王太, 张艳萍, 管丽红, 杜岩岩, 娄忠玉, 焦文龙. 甘肃省鱼类资源现状及DNA条形码在鱼类物种鉴定中的应用. 生物多样性, 2015, 23(3): 306-313. http://www.biodiversity-science.net/CN/article/downloadArticleFile.do?attachType=PDF&id=10015 附录1 甘肃省鱼类种类组成 Appendix 1 Fish species composition in Gansu Province 目 Order 科 Family 属 Genus 种 Species 鲑形目 Salmoniformes 鲑科 Salmonidae 细鳞鲑属 Brachymystax 秦岭细鳞鲑 Brachymystax lenok tsinlingensis 公鱼属 Hypomesus 池沼公鱼 Hypomesus olidus 鲇形目 Siluriformes 鲇科 Siluridae 鲇属 Silurus 鲇鱼 Silurus asotus 怀头鲶 Silurus soldatovi 鮡科 Sisoridae 鮡属 Pareuchiloglanis 前臀鮡 Pareuchiloglanis anteanalis 纹胸鮡属 Glyptothorax 中华纹胸鮡 Glyptothorax sinense 鲿科 Bagridae 拟鲿属 Pseudobagrus 切尾拟鲿 Pseudobagrus truncatus 鱯属 Mystus 大鳍鱯 Mystus macropterus 鲈形目 Perciformes 鰕虎鱼科 Gobiidae 吻鰕虎鱼属 Rhinogobius 褐吻鰕虎鱼 Rhinogobius brunneus 塘鳢科 Hypseleotris 黄黝鱼属 Hypseleotris 黄黝鱼 Hypseleotris swinhonis 合鳃鱼目 Symbranchiformes 合鳃鱼科 Synbranchidae 黄鳝属 Monopterus 黄鳝 Monopterus albus 鲤形目 Cypriniformes 鲤科 Cyprinidae 鰟鮍属 Rhodeus 高体鰟鮍 Rhodeus ocellatus 棒花鱼属 Abbottina 棒花鱼 Abbottina rivularis 颌须鮈属 Gnathopogon 嘉陵颌须鮈 Gnathopogon herzensteini 短须颌须鮈 Gnathopogon imberbis 胡鮈属 Huigobio 清徐胡鮈 Huigobio chinssuensis 鮈属 Gobio 黄河鮈 Gobio huanghensis 似铜鮈 Gobio coriparoides 蛇鮈属 Saurogobio 蛇鮈 Saurogobio dabryi 似鮈属 Pseudogobio 似鮈 Pseudogobio vaillanti 片唇鮈属 Platysmacheilus 裸腹片唇鮈 Platysmacheilus nudiventris 麦穗鱼属 Pseudorasbora 麦穗鱼 Pseudorasbora parva 属 Hemibarbus 唇 Hemibarbus labeo 花 Hemibarbus maculatus 似 属 Belligobio 似 Belligobio nummifer 马口鱼属 Opsariichthys 马口鱼 Opsariichthys bidens 鱲属 Zacco 宽鳍鱲 Zacco platypus 属 Phoxinus 拉氏 Phoxinus lagowskii 尖头 Phoxinus -
De Novo Assembly of Schizothorax Waltoni Transcriptome to Identify Immune-Related Genes Cite This: RSC Adv.,2018,8, 13945 and Microsatellite Markers†
RSC Advances View Article Online PAPER View Journal | View Issue De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes Cite this: RSC Adv.,2018,8, 13945 and microsatellite markers† Hua Ye,ab Zhengshi Zhang,ab Chaowei Zhou,ab Chengke Zhu,ab Yuejing Yang,ab Mengbin Xiang,ab Xinghua Zhou,ab Jian Zhou*c and Hui Luo *ab Schizothorax waltoni (S. waltoni) is one kind of the subfamily Schizothoracinae and an indigenous economic tetraploid fish to Tibet in China. It is rated as a vulnerable species in the Red List of China's Vertebrates, owing to overexploitation and biological invasion. S. waltoni plays an important role in ecology and local fishery economy, but little information is known about genetic diversity, local adaptation, immune system and so on. Functional gene identification and molecular marker development are the first and essential step for the following biological function and genetics studies. For this purpose, the transcriptome from pooled tissues of three adult S. waltoni was sequenced and Creative Commons Attribution-NonCommercial 3.0 Unported Licence. analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83 103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66 975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58 934, 87.99%) were successfully annotated by 7 public databases, and 15 KEGG pathways of immune-related genes were identified for the following functional research. Furthermore, 19 497 putative simple sequence repeats (SSRs) of 1–6 bp unit length were detected from 14 690 unigenes (21.93%) with an average distribution density of 1 : 3.28 kb. -
Resolving Cypriniformes Relationships Using an Anchored Enrichment Approach Carla C
Stout et al. BMC Evolutionary Biology (2016) 16:244 DOI 10.1186/s12862-016-0819-5 RESEARCH ARTICLE Open Access Resolving Cypriniformes relationships using an anchored enrichment approach Carla C. Stout1*†, Milton Tan1†, Alan R. Lemmon2, Emily Moriarty Lemmon3 and Jonathan W. Armbruster1 Abstract Background: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). Results: Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. Conclusions: Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited. Keywords: Fish, High-throughput -
From Kunlun Pass Basin, Northeastern Tibetan Plateau and Their Bearings on Development of Water System and Uplift of the Area
SCIENCE CHINA Earth Sciences • RESEARCH PAPER • April 2010 Vol.53 No.4: 485–500 doi: 10.1007/s11430-010-0048-5 Pliocene cyprinids (Cypriniformes, Teleostei) from Kunlun Pass Basin, northeastern Tibetan Plateau and their bearings on development of water system and uplift of the area WANG Ning & CHANG Mee-mann* Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China Received November 23, 2009; accepted February 25, 2010 Here described are the cyprinid fossils from the Pliocene Lower Member of Qiangtang Formation of the Kunlun Pass Basin, northeastern Tibetan Plateau, collected at a locality 4769 m above the sea level (asl). The materials consist of numerous disar- ticulated and incomplete bones as well as thousands of pharyngeal teeth, fin rays, and vertebrae. The fossils were referred to the genus Gymnocypris, lineage Schizothoracini, family Cyprinidae; the lineage Schizothoracini; and the family Cyprinidae respectively. The Schizothoracini is a freshwater fish group endemic to the Tibetan Plateau and its surrounding area. Previous workers on living schizothoracins regarded that Gymnocypris belongs to the highly specialized grade of the group, colonizing higher altitudes than other members of the group. Two species are so far unequivocally assigned to the genus, i.e., G. przewalskii and G. eckloni, and they are inhabiting Qinghai Lake and the waters on both north (the Golmud River) and south (upper reach of the Yellow River) sides of the East Kunlun Mountain, respectively. The abundant fossil schizothoracins occur in the Kunlun Pass Basin on the southern slope of the East Kunlun Mountain (at 4769 m asl), close to the present Golmud River, indicating comparatively rich waters in the area and possible connections between the water systems on north and south sides of the East Kunlun Mountain during the Pliocene. -
Teleostei: Cypriniformes: Cyprinidae) Inferred from Complete Mitochondrial Genomes
Biochemical Systematics and Ecology 64 (2016) 6e13 Contents lists available at ScienceDirect Biochemical Systematics and Ecology journal homepage: www.elsevier.com/locate/biochemsyseco Molecular phylogeny of the subfamily Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) inferred from complete mitochondrial genomes * Jie Zhang a, b, Zhuo Chen a, Chuanjiang Zhou b, Xianghui Kong b, a College of Life Science, Henan Normal University, Xinxiang 453007, PR China b College of Fisheries, Henan Normal University, Xinxiang 453007, PR China article info abstract Article history: The schizothoracine fishes, members of the Teleost order Cypriniformes, are one of the Received 16 June 2015 most diverse group of cyprinids in the QinghaieTibetan Plateau and surrounding regions. Received in revised form 19 October 2015 However, taxonomy and phylogeny of these species remain unclear. In this study, we Accepted 14 November 2015 determined the complete mitochondrial genome of Schizopygopsis malacanthus. We also Available online xxx used the newly obtained sequence, together with 31 published schizothoracine mito- chondrial genomes that represent eight schizothoracine genera and six outgroup taxa to Keywords: reconstruct the phylogenetic relationships of the subfamily Schizothoracinae by different Mitochondrial genome Phylogeny partitioned maximum likelihood and partitioned Bayesian inference at nucleotide and fi Schizothoracinae amino acid levels. The schizothoracine shes sampled form a strongly supported mono- Schizopygopsis malacanthus phyletic group that is the sister taxon to Barbus barbus. A sister group relationship between the primitive schizothoracine group and the specialized schizothoracine group þ the highly specialized schizothoracine group was supported. Moreover, members of the specialized schizothoracine group and the genera Schizothorax, Schizopygopsis, and Gym- nocypris were found to be paraphyletic. © 2015 Published by Elsevier Ltd. -
The Nu River: a Habitat in Danger Krystal Chen, International Rivers
The Nu River: A Habitat in Danger Krystal Chen, International Rivers The Nu River is an important freshwater ecological system in Nu River (NFGRPA) was established in 2010, and approved by southwestern China. It boasts a wealth of fish species, more than 40 % the Ministry of Agriculture. The protected area covers 316 km of of which are endemic to the region. The region is worth protecting the Nu’s main stream and tributaries in the Nu Prefecture, where for its immense value to biodiversity research. However, the number seven species have been chosen as key protected species, including of fish species in the Nu has seen a sharp decrease in recent years, Schizothorax nukiangensis, Schizothorax gongshanensis, Tor hemispinus, and big fish are found and caught much less often. Overfishing and Placocheilus cryptonemus, Anguilla nebulosi, Akrokolioplax bicornis, and ecological degradation have been cited as possible causes. With five Pareuchiloglanis gongshanensis. Fifteen other species endemic to the Nu cascading hydropower stations planned in the upper and middle are also protected. reaches of the Nu, fish species in the Nu River now face alarming ZHENG Haitao conducted a preliminary analysis on the Index of threats. Biological Integrity (IBI) of the fish species in the upper and middle Fish biodiversity in the Nu River Region reaches of the Nu in 2004. The result showed that the integrity of fish species in the area is in good condition with low human intervention. According to CHEN Xiaoyong’s Fish Directory in Yunnan1 and Constraints mainly come from natural elements, such as habitat type other recent research2 conducted by his team, 62 species from 12 and food availability. -
Age Structure and Growth Characteristics of the Endemic Fish
Zoological Studies 50(1): 69-75 (2011) Age Structure and Growth Characteristics of the Endemic Fish Oxygymnocypris stewartii (Cypriniformes: Cyprinidae: Schizothoracinae) in the Yarlung Tsangpo River, Tibet Yin-Tao Jia1,2 and Yi-Feng Chen1,* 1Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2Graduate School of Chinese Academy of Sciences, Beijing 100039, China (Accepted September 10, 2010) Yin-Tao Jia and Yi-Feng Chen (2011) Age structure and growth characteristics of the endemic fish Oxygymnocypris stewartii (Cypriniformes: Cyprinidae: Schizothoracinae) in the Yarlung Tsangpo River, Tibet. Zoological Studies 50(1): 69-75. The age structure and growth characteristics of Oxygymnocypris stewartii were studied using 430 specimens collected from the Yarlung Tsangpo River, Tibet. Our study on the length-frequency and age structure indicated that this population was suffering from unreasonable exploitation. The standard length (SL; mm)-body weight (W; g) relationship was W = 1.30 × 10-5 SL3.002. The SL (Lt)- and weight (Wt)-at-age relationships were described by von Bertalanffy growth functions -0.1069 (t - 0.5728) -0.1069 (t - 0.5728) 2.997 as follows: Lt = 877.4821[1 - e ] and Wt = 8805.1493[1 - e ] for females, and -0.1686(t - 0.6171) -0.1686(t - 0.6171) 3.098 Lt = 599.3939[1 - e ] and Wt = 3091.3496[1 - e ] for males. It was observed that O. stewartii grew faster during the 1st 3 yr than other schizothoracines inhabiting the same region, and then its growth became slower. Our study also indicated that (1) O. stewartii’s growth performance was relatively higher than those of other schizothoracines which inhabit the same region, and (2) its growth performance was relatively lower than those of other piscivore Cyprinidae fishes such as Culter alburnus Basilewsky which inhabit Wu and Cheng Lakes. -
Indian Museum
RECQ'RDS oftbe INDIAN MUSEUM (1\ JOURN1\L Of INOI"N ZOOLOGY) Vol. VI, 1'911. EDITED BY TI1E SU ERI! TENDEN1' OF THE IN DIA~ l\IUSEU L (!,nlcutta : P BLISHED B - ORDER OF THE TRUSTEES OF THE INDIA MUSBUl\I, BAPTI~T MISS! ,N PRE&<;. , 9(~· CONTENTS. -¢-- PART I, MARCIl. I. Note 'on a Rhizocephalous Crustacean from fre~b water and on some specimens of the order from Indian seas .• I II. Notes on D capoda in the Indian Museum II.~Descriptions of two new Crangollidae 'With observations ou the mutual affiniti·es of the genera POlltOPhil1,tssl1d PkUochertlS 5 TIT. Contributions to theauna 0" Yunnan- Part II.-Fishes 13 ., III. ~ Butterflies 25 " IV.-Les Chirollomides (Teauipedidae) 27 " V.- Bihionidae , l\{ycetophilidae and Ano- phelinae 31 IV. Notes on Pe lipalpi in the collection of the Indian Mllseum~ L~New P dipalpi from Calcutta 33 II . ~A prelinlinary note on a new S(u',a ~ from Siugapore 36 v. Descriptions of six new species of sbell ~ from Bengal and Madras 39 Miscellanea {PI>. 43-40) ;- Report on a smal collection of fleas from India and China 43 Some tHes found associate 1 with cattle III the neigbbourhood of Calcutta 44 Mosquito sucked by a midge 45 Large egg laid hy a beetl .. 45 P AR'i' II, :\1 A Y. VI. Some Sponges associated with gregalious i\iolius<:s of the family Vennetidae 47 VII. Report on acoUection of aquatic animals made in Tibet by Captain F. H. Stewart, I ..:\I.S., during the year 1907- Part III -Turbellaria 57 List of the aquatic animals hitherto recorded from the provinces of 'I'sang andU in C.el tral Tibet. -
Phylogeny of the Specialized Schizothoracine Fishes (Teleostei: Cypriniformes: Cyprinidae)
Zoological Studies 40(2): 147-157 (2001) Phylogeny of the Specialized Schizothoracine Fishes (Teleostei: Cypriniformes: Cyprinidae) Zi-Ming Chen1,2 and Yi-Feng Chen1,* 1Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China 2Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China (Accepted January 30, 2001) Zi-Ming Chen and Yi-Feng Chen (2001) Phylogeny of the specialized schizothoracine fishes (Teleostei: Cypriniformes: Cyprinidae). Zoological Studies 40(2): 147-157. To elucidate phylogenetic relationships within the specialized schizothoracine fishes, we used 41 variable osteological and external characters among this groups, three species of Schizothorax, and 1 fossil species. When the 3 species of Schizothorax were desig- nated as an outgroup and all 41 characters were set as unordered with equal weighting, the data matrix yielded a single most-parsimonious tree with a tree length of 71 steps, a consistency index of 0.6761, and a retention index of 0.7416. Meanwhile, a bootstrap test was conducted to verify the reliability of the results. The matrix was also analyzed for different conditions: all characters were ordered and the fossil species was added as an outgroup. The phylogenetic analyses presented herein support the following hypotheses. 1) All species of the specialized schizo-thoracines fishes form a monophyletic group. 2) Monophyly of the genus Ptychobarbus is not supported by the bootstrap test or when these characters are ordered. 3) The genus Gymnodiptychus forms a monophyletic group. 4) All species of Ptychobarbus and Gymnodiptychus form a monophyletic group with Diptychus as its sister group. Key words: Cyprinidae, Specialized schizothoracine fishes, Character analysis, Phylogenetic relationships, Tibetan Plateau. -
And Adaptive Evolution in Their Mitochondrial Genomes
Genes Genet. Syst. (2014) 89, p. 187–191 Polyphyletic origins of schizothoracine fish (Cyprinidae, Osteichthyes) and adaptive evolution in their mitochondrial genomes Takahiro Yonezawa1,2, Masami Hasegawa1,2 and Yang Zhong1,3* 1School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai 200438, China 2The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa, Tokyo 190-8562, Japan 3Institute of Biodiversity Science and Geobiology, Tibet University, JiangSu Rd. 36, Lhasa, 850000, China (Received 25 July 2014, accepted 9 October 2014) The schizothoracine fish, also called snow trout, are members of the Cyprinidae, and are the most diversified teleost fish in the Qinghai-Tibetan Plateau (QTP). Clarifying the evolutionary history of the schizothoracine fish is therefore important for better understanding the biodiversity of the QTP. Although mor- phological and molecular phylogenetic studies have supported the monophyly of the Schizothoracinae, a recent molecular phylogenetic study based on the mito- chondrial genome questioned the monophyly of this taxon. However, the phylo- genetic analysis of that study was on the basis of only three schizothoracine species, and the support values were low. In this report, we inferred the phylo- genetic tree on the basis of mitochondrial genome data including 21 schizothora- cine species and five closely related species, and the polyphyletic origins of the Schizothoracinae were strongly supported. The tree further suggests that the Schizothoracinae consists of two clades, namely the “morphologically specialized clade” and the “morphologically primitive clade”, and that these two clades migrated independently of each other to the QTP and adapted to high altitude. We also detected in their mitochondrial genomes strong signals of posi- tive selection, which probably represent evidence of high-altitude adaptation. -
De Novo Transcriptome Assembly and Positive Selection Analysis of An
Lan et al. BMC Genomics (2018) 19:394 https://doi.org/10.1186/s12864-018-4720-z RESEARCHARTICLE Open Access De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish Yi Lan1, Jin Sun1, Ting Xu2, Chong Chen3, Renmao Tian1, Jian-Wen Qiu2 and Pei-Yuan Qian1* Abstract Background: High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives. Results: We captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod. Conclusions: Overall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea.