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Lin et al. BMC Genomics 2014, 15:32 http://www.biomedcentral.com/1471-2164/15/32 RESEARCH ARTICLE Open Access Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia) Gong-Hua Lin1, Kun Wang2, Xiao-Gong Deng1,3, Eviatar Nevo4, Fang Zhao1, Jian-Ping Su1, Song-Chang Guo1, Tong-Zuo Zhang1* and Huabin Zhao5* Abstract Background: Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incongruence of molecular evidence, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performed de novo transcriptome sequencing of four RNA-seq libraries prepared from brain and liver tissues of a plateau zokor (Eospalax baileyi) and a hoary bamboo rat (Rhizomys pruinosus), and analyzed the transcriptome sequences alongside a published transcriptome of the Middle East blind mole rat (Spalax galili). We characterize the transcriptome assemblies of the two spalacids, and recover the phylogeny of the three subfamilies using a phylogenomic approach. Results: Approximately 50.3 million clean reads from the zokor and 140.8 million clean reads from the bamboo ratwere generated by Illumina paired-end RNA-seq technology. All clean reads were assembled into 138,872 (the zokor) and 157,167 (the bamboo rat) unigenes, which were annotated by the public databases: the Swiss-prot, Trembl, NCBI non-redundant protein (NR), NCBI nucleotide sequence (NT), Gene Ontology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). -
Tissue Specific Regulatory Network Annotation for Non-Coding Elements
Quantitative Biology 2020, 8(1): 43–50 https://doi.org/10.1007/s40484-020-0195-4 RESEARCH ARTICLE ZokorDB: tissue specificregulatorynetwork annotation for non-coding elements of plateau zokor Jingxue Xin1,6,7,†, Junjun Hao2,†, Lang Chen1, Tao Zhang3, Lei Li1,5,7, Luonan Chen3,5, Wenmin Zhao4, Xuemei Lu2,5, Peng Shi2,5,*, Yong Wang1,5,7,* 1 CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China 2 State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 3 Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China 5 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China 6 Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA 7 University of Chinese Academy of Sciences, Beijing 100049, China * Correspondence: [email protected], [email protected] Received September 4, 2019; Revised December 16, 2019; Accepted December 23, 2019 Background: Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration. Methods: We provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. -
Taxonomy and Phylogenetic Relationship of Zokors
Journal of Genetics (2020)99:38 Ó Indian Academy of Sciences https://doi.org/10.1007/s12041-020-01200-2 (0123456789().,-volV)(0123456789().,-volV) RESEARCH ARTICLE Taxonomy and phylogenetic relationship of zokors YAO ZOU1, MIAO XU1, SHIEN REN1, NANNAN LIANG1, CHONGXUAN HAN1*, XIAONING NAN1* and JIANNING SHI2 1Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling 712100, People’s Republic of China 2Ningxia Hui Autonomous Region Forest Disease and Pest Control Quarantine Station, Yinchuan 750001, People’s Republic of China *For correspondence. E-mail: Chongxuan Han, [email protected]; Xiaoning Nan, [email protected]. Received 24 October 2019; revised 19 February 2020; accepted 2 March 2020 Abstract. Zokor (Myospalacinae) is one of the subterranean rodents, endemic to east Asia. Due to the convergent and parallel evolution induced by its special lifestyles, the controversies in morphological classification of zokor appeared at the level of family and genus. To resolve these controversies about taxonomy and phylogeny, the phylogenetic relationships of 20 species of Muroidea and six species of zokors were studied based on complete mitochondrial genome and mitochondrial Cytb gene, respectively. Phylogeny analysis of 20 species of Muroidea indicated that the zokor belonged to the family Spalacidae, and it was closer to mole rat rather than bamboo rat. Besides, by investigating the phylogenetic relationships of six species of zokors, the status of two genera of Eospalax and Myospalax was affirmed because the two clades differentiated in phylogenetic tree represented two types of zokors, convex occiput type and flat occiput type, respectively. -
Chapter 4 the Antiquity of Rhizomys and Independent Acquisition of Fossorial Traits in Subterranean Muroids
Chapter 4 The Antiquity of Rhizomys and Independent Acquisition of Fossorial Traits in Subterranean Muroids LAWRENCE J. FLYNN1 ABSTRACT In parallel with the growing body of molecular data bearing on the relationships of muroids, particularly subterranean lineages, the relevant fossil record has improved to the point that its data constrain scenarios of evolution about both the timing and mode of evolution of burrowing muroids, especially bamboo rats, blind mole rats, and zokors. Morphologists have considered these groups phylogenetically distinct from each other, but the three lineages appear to be related as a monophyletic Family Spalacidae, sister taxon to all other living muroids, based on both nuclear and mitochondrial genes. Although living genera are fully subterranean, the fossil record shows that the three groups evolved burrowing characteristics independently. Bamboo rats (Rhizomyinae) have the longest fossil record, extending into the Late Oligocene, but do not show fossorial traits until the Late Miocene. Blind mole rats (Spalacinae) have a fossil record nearly that long, and its early members also lack burrowing traits. Zokors (Myospalacinae) show characteristics considered derived relative to other groups, and have a shorter fossil record. The fossil record of the Tribe Rhizomyini, living Asian bamboo rats, extends to about 10 million years ago, with early species distinct at the generic level from living Rhizomys. The oldest well- known species assignable to an extant genus is Rhizomys (Brachyrhizomys) shansius from the early Pliocene of Yushe Basin, China, north of the geographic range of modern Rhizomys.A hypothesis of close relationship of bamboo rats, blind mole rats, and zokors leads to a reevaluation of affinities of certain Asian fossil taxa and reevaluation of polarity of some features, but molecular data are not yet robust enough to clarify interrelationships of the groups. -
Hystrx It. J. Mamm. (Ns) Supp. (2007) V European Congress of Mammalogy
Hystrx It. J. Mamm . (n.s.) Supp. (2007) V European Congress of Mammalogy RODENTS AND LAGOMORPHS 51 Hystrx It. J. Mamm . (n.s.) Supp. (2007) V European Congress of Mammalogy 52 Hystrx It. J. Mamm . (n.s.) Supp. (2007) V European Congress of Mammalogy A COMPARATIVE GEOMETRIC MORPHOMETRIC ANALYSIS OF NON-GEOGRAPHIC VARIATION IN TWO SPECIES OF MURID RODENTS, AETHOMYS INEPTUS FROM SOUTH AFRICA AND ARVICANTHIS NILOTICUS FROM SUDAN EITIMAD H. ABDEL-RAHMAN 1, CHRISTIAN T. CHIMIMBA, PETER J. TAYLOR, GIANCARLO CONTRAFATTO, JENNIFER M. LAMB 1 Sudan Natural History Museum, Faculty of Science, University of Khartoum P. O. Box 321 Khartoum, Sudan Non-geographic morphometric variation particularly at the level of sexual dimorphism and age variation has been extensively documented in many organisms including rodents, and is useful for establishing whether to analyse sexes separately or together and for selecting adult specimens to consider for subsequent data recording and analysis. However, such studies have largely been based on linear measurement-based traditional morphometric analyses that mainly focus on the partitioning of overall size- rather than shape-related morphological variation. Nevertheless, recent advances in unit-free, landmark/outline-based geometric morphometric analyses offer a new tool to assess shape-related morphological variation. In the present study, we used geometric morphometric analysis to comparatively evaluate non-geographic variation in two geographically disparate murid rodent species, Aethmoys ineptus from South Africa and Arvicanthis niloticus from Sudan , the results of which are also compared with previously published results based on traditional morphometric data. Our results show that while the results of the traditional morphometric analyses of both species were congruent, they were not sensitive enough to detect some signals of non-geographic morphological variation. -
Ecologically-Based Management of Rodent Pests ECOLOGICALL V-BASED MANAGEMENT of RODENT PESTS
Ecologically-based Management of Rodent Pests ECOLOGICALL V-BASED MANAGEMENT OF RODENT PESTS Edited by: Grant R. Singleton, Lyn A. Hinds, Herwig Leirs and Zhibin Zhang Australian Centre for International Agricultural Research Canberra 1999 The Australian Centre for International Agricultural Research (ACIAR) was established in June 1982 by an Act of the Australian Parliament. Its primary mandate is to help identify agricultural problems in developing countries and to commission collaborative research between Australian and developing country researchers in fields where Australia has special competence. Where trade names are used this constitutes neither endorsement of nor discrimination against any product by the Centre. ACIAR MONOGRAPH SERIES This peer-reviewed series contains the results of original research supported by ACIAR, or deemed relevant to ACIAR's research objectives. The series is distributed internationally, with an emphasis on the Third World ©Australian Centre for International Agricultural Research GPO Box Canberra, ACT 2601. Singleton, C.R., Hinds, L.A., Leirs, H. and Zhang, Z.ed. 1999. Ecologically-based management of rodent ACIAR Monograph No. 59, 494p. ISBN 1 86320 262 5 Editing and design by Arawang Communication Croup, Canberra Printed by Brown Prior Anderson, Melbourne, Australia page Author Contact Details 8 Abbreviations 12 List of Species 13 Preface 15 1. Ecologically-based Management of Rodent Pests-Re-evaluating 17 Our Approach to an Old Problem Grant R. Singleton, Herwig Leirs, Lyn A. Hinds and Zhibin Zhang Section 1 Basic Research - the Foundation for Sound Management 31 2. Current Paradigms of Rodent Population Dynamics- 33 What Are We Missing? Charles J. Krebs 3. The Behaviour and Ecology of Rattus norvegicus: from Opportunism to 49 Kamikaze Tendencies David W. -
List of 28 Orders, 129 Families, 598 Genera and 1121 Species in Mammal Images Library 31 December 2013
What the American Society of Mammalogists has in the images library LIST OF 28 ORDERS, 129 FAMILIES, 598 GENERA AND 1121 SPECIES IN MAMMAL IMAGES LIBRARY 31 DECEMBER 2013 AFROSORICIDA (5 genera, 5 species) – golden moles and tenrecs CHRYSOCHLORIDAE - golden moles Chrysospalax villosus - Rough-haired Golden Mole TENRECIDAE - tenrecs 1. Echinops telfairi - Lesser Hedgehog Tenrec 2. Hemicentetes semispinosus – Lowland Streaked Tenrec 3. Microgale dobsoni - Dobson’s Shrew Tenrec 4. Tenrec ecaudatus – Tailless Tenrec ARTIODACTYLA (83 genera, 142 species) – paraxonic (mostly even-toed) ungulates ANTILOCAPRIDAE - pronghorns Antilocapra americana - Pronghorn BOVIDAE (46 genera) - cattle, sheep, goats, and antelopes 1. Addax nasomaculatus - Addax 2. Aepyceros melampus - Impala 3. Alcelaphus buselaphus - Hartebeest 4. Alcelaphus caama – Red Hartebeest 5. Ammotragus lervia - Barbary Sheep 6. Antidorcas marsupialis - Springbok 7. Antilope cervicapra – Blackbuck 8. Beatragus hunter – Hunter’s Hartebeest 9. Bison bison - American Bison 10. Bison bonasus - European Bison 11. Bos frontalis - Gaur 12. Bos javanicus - Banteng 13. Bos taurus -Auroch 14. Boselaphus tragocamelus - Nilgai 15. Bubalus bubalis - Water Buffalo 16. Bubalus depressicornis - Anoa 17. Bubalus quarlesi - Mountain Anoa 18. Budorcas taxicolor - Takin 19. Capra caucasica - Tur 20. Capra falconeri - Markhor 21. Capra hircus - Goat 22. Capra nubiana – Nubian Ibex 23. Capra pyrenaica – Spanish Ibex 24. Capricornis crispus – Japanese Serow 25. Cephalophus jentinki - Jentink's Duiker 26. Cephalophus natalensis – Red Duiker 1 What the American Society of Mammalogists has in the images library 27. Cephalophus niger – Black Duiker 28. Cephalophus rufilatus – Red-flanked Duiker 29. Cephalophus silvicultor - Yellow-backed Duiker 30. Cephalophus zebra - Zebra Duiker 31. Connochaetes gnou - Black Wildebeest 32. Connochaetes taurinus - Blue Wildebeest 33. Damaliscus korrigum – Topi 34. -
Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2009 Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Recommended Citation Norris, Ryan, "Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils" (2009). Graduate College Dissertations and Theses. 164. https://scholarworks.uvm.edu/graddis/164 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. PHYLOGENETIC RELATIONSHIPS AND DIVERGENCE TIMES IN RODENTS BASED ON BOTH GENES AND FOSSILS A Dissertation Presented by Ryan W. Norris to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Biology February, 2009 Accepted by the Faculty of the Graduate College, The University of Vermont, in partial fulfillment of the requirements for the degree of Doctor of Philosophy, specializing in Biology. Dissertation ~xaminationCommittee: w %amB( Advisor 6.William ~il~atrickph.~. Duane A. Schlitter, Ph.D. Chairperson Vice President for Research and Dean of Graduate Studies Date: October 24, 2008 Abstract Molecular and paleontological approaches have produced extremely different estimates for divergence times among orders of placental mammals and within rodents with molecular studies suggesting a much older date than fossils. We evaluated the conflict between the fossil record and molecular data and find a significant correlation between dates estimated by fossils and relative branch lengths, suggesting that molecular data agree with the fossil record regarding divergence times in rodents. -
Phylogenetic Relationships Between Zokors Myospalax
PROCEEDINGS OF THE LATVIAN ACADEMY OF SCIENCES. Section B, Vol. 74 (2020), No. 1 (724), pp. 25–34. DOI: 10.2478/prolas-2020-0005 PHYLOGENETIC RELATIONSHIPS BETWEEN ZOKORS MYOSPALAX (MAMMALIA, RODENTIA) DETERMINED ON THE BASIS OF MORPHOMETRIC AND MOLECULAR ANALYSES Dalius Butkauskas1,#, Marija Starodubaitë1, Mikhail Potapov2, Olga Potapova2, Sergei Abramov2, and Yury Litvinov2 1 Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, LITHUANIA 2 Institute of Systematics and Ecology of Animals Siberian Branch of Russian Academy of Science, 11 Frunze Str., Novosibirsk, 630091, RUSSIA # Corresponding author, [email protected] Communicated by Isaak Rashal Phylogenetic relationships between zokors living in different territories of Russia: Altai zokors Myospalax myospalax from “Altai” (Altai Republic and Altaiskii Krai) and “Priobie” from the River Ob zone (Tomsk oblast and Novosibirsk oblast) and subspecies M. m. tarbagataicus from Ka- zakhstan (ridge Tarbagatai) and M. aspalax and M. psilurus from Zabaikalskii Krai were deter- mined on the basis of craniometrical and molecular analysis of the mitochondrial 12S rRNA gene. The comparison of the craniometrical and molecular data revealed significant differences be- tween the Altai zokors of the “Priobie” (the River Ob zone) and “Altai” populations. The impor- tance of geographic isolation to the formation of morphometric and genetic differentiation of distinct geographic forms of the investigated zokors is shown. Specific ecological and morphologi- cal adaptations and distinct genetic features of two forms of zokors indicate the existence of separate subspecies of the species M. myospalax. Key words: Myospalacinae, Myospalax spp., Altai zokor, craniometric analysis, systematics, molecular-genetic variability. INTRODUCTION zokors became extinct or were forced to migrate due to changing climatic conditions. -
Downloaded from Brill.Com10/04/2021 09:40:17AM Via Free Access 290 Z
Animal Biology 68 (2018) 289–308 brill.com/ab p53 gene cloning and response to hypoxia in the plateau zokor, Myospalax baileyi Zhi-fang An1,2,+, Kang Zhao3,+, Lin-na Wei4, Zhi-jie Wang4, Su-hua Li2, Lian Wei4 and Deng-bang Wei1,4,∗ 1 State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China 2 Research Center for High Altitude Medicine, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China 3 College of Medical, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China 4 College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China Submitted: January 5, 2018. Final revision received: March 3, 2018. Accepted: April 2, 2018 Abstract The plateau zokor (Myospalax baileyi) is a specialized subterranean rodent that lives on the Qinghai- Tibet Plateau. The species has evolved a series of strategies to adapt to its hypoxic environment and hypercapnia. p53 is a tumour suppressor gene that plays a crucial role in the cellular response to hypoxia by inducing cell cycle arrest, cell apoptosis, DNA damage repair and angiogenesis. To inves- tigate the sequence characteristics of p53 and the response to hypoxia in plateau zokor, we cloned the p53 coding DNA sequence, analysed it, and measured the expression level of p53 at different altitudes in plateau zokor and rats. Our results show that the coding DNA sequence is 1179 bp, consisting of 392 amino acid residues. Compared to human p53, the subterranean rodents have two mutation sites in common with the human hotspots in the DNA-binding domain. -
The First Finding of Mimomys in the Russian Far East
The first finding of Mimomys in the Russian Far East MIKHAIL P. TIUNOV, FEDOR N. GOLENISHCHEV, and LEONID L. VOYTA A new species of the Mimomys is described from the Far East Holocene and Late Pleistocene deposits of the Bliznets Cave, Russia (the Medvezhyi Klyk cave, Sikhote-Alin). Layer 7 of which is known as the richest paleontological site of its type in the Medvezhyi Klyk cave (1.08–1.18 m) was dated to be 13 the south of the Russian Far East (Tiunov 1976; Alexeeva 1986; 790–14 200 BP. Mimomys chandolensis sp. nov. was found in Alexeeva and Golenishchev 1986; Tiunov et al. 1992; Alexeeva a deeper layer (2.63–2.68 m) and therefore assuming there 2007). The other site that is of equal interest is the Medvezhyi was no redeposition of the remains and that the accumula- Klyk cave (Тiunov and Panasenko 2007), where tens of thou- tion proceeded gradually, the molar specimen we found is sands of amphibian, reptilian, avian and mammalian fossil re- 30–50 kyr old. Due to the extent of the preservation we ob- mains were collected between 2005 and 2009 (Panasenko and served in the molar and the structure of the cave, the spec- Тiunov 2010; Тiunov and Panasenko 2010) including a single imen does not seem likely to have been redeposited. Our tooth of Mimomys that is a subject of this paper. hypothesis is that due to the warm and wet climate of the Institutional abbreviations.—GIN, Geological Institute, Rus- region, the vole, which became extinct more than 600 kyr sian Academy of Sciences, Moscow, Russia; ZIN, Zoolo gical ago, had been extant there by the Late Pleistocene period. -
Myospalax Baileyi) from the Qinghai-Tibet Plateau
Article Animal Genetics March 2012 Vol.57 No.9: 9971006 doi: 10.1007/s11434-011-4911-3 SPECIAL TOPICS: cDNA cloning and expression of erythropoietin in the plateau zokor (Myospalax baileyi) from the Qinghai-Tibet Plateau WANG ZhenLong1,2†, CHEN Yan3,4†, YANG Jie5, CHEN WeiJun3*, ZHANG YanMing2* & ZHAO XinQuan2* 1 Department of Bioengineering, Zhengzhou University, Zhengzhou 450001, China; 2 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China; 3 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; 4 Graduate University of the Chinese Academy of Sciences, Beijing 100049, China; 5 Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang 050017, China Received August 15, 2011; accepted September 23, 2011 All organisms respond to variation in their environments and manage environmental stress through metabolic adjustments. The plateau zokor (Myospalax baileyi) is an endemic and keystone subterranean rodent species that inhabits the Qinghai-Tibet Plateau between 2800 and 4200 m above sea level. It is a hypoxic-tolerant mammal with a high ratio of oxygen utilization that enables it to cope with its harsh surroundings. To explore the molecular mechanism of altitude acclimatization of the plateau zokor, we cloned the zokor erythropoietin (Epo) gene and used real-time PCR to compare Epo mRNA levels in zokors inhabiting 16 differ- ent altitudes. The full-length zokor Epo open reading frame was 579 bp that encoded a precursor peptide of 192 amino acids with a signal peptide of 26 residues. The Epo gene of the plateau zokor was 81%–95% homologous to that of human, mouse, rat, root vole and the Golan Heights blind mole rat, with the highest homology (95%) to species of the genus Spalax.