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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Faria AR, Nunes JB, Leite ALL, Ramos ABDSB, Siqueira RV, Nogueira ESC, Marques MJ, Colombo FA. Risk of Trypanosoma cruzi transmission in southern Minas Gerais, Brazil - Data from 2014 to 2020. VETERINARY PARASITOLOGY- REGIONAL STUDIES AND REPORTS 2021; 23:100530. [PMID: 33678384 DOI: 10.1016/j.vprsr.2021.100530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 11/27/2022]
Abstract
Trypanosoma cruzi, the etiologic agent of Chagas disease, is widely distributed in the Americas and is transmitted through vectorial, transfusional, and oral routes. This study aimed to evaluate the risk of vectorial transmission of Chagas disease in municipalities located in southern Minas Gerais, Brazil, by analyzing triatomine specimens collected from 2014 to 2020. All 1522 hematophagous triatomines were identified as Panstrongylus megistus, and were subjected to parasitological and molecular examinations. From 2014 to 2016, approximately 10% of insects were positive in the microscopic analysis of intestinal content, and 27% were positive as detected by the quantitative polymerase chain reaction (qPCR) of the same sampling. However, in the last investigated years, an increase in infected triatomines was observed in microscopic analysis (22%) and qPCR methods (41%). This corroborates the findings of acute human Chagas disease cases, which have increased in the study area from a maximum of 2 cases in previous years to 20 cases in 2019, and 17 cases in 2020 through June. Additionally, bloodmeal sources of infected triatomines were investigated; human blood was detected in up to 85.7% of the samples. Moreover, canine blood was also detected in triatomine intestinal content in recent years, reaching 91% of analyzed insects in 2018. Data on bloodmeal sources have demonstrated human-vector contact and have suggested the participation of dogs in the parasite transmission cycle. These results indicate the risk of T. cruzi vectorial transmission in Southern Minas Gerais and São Paulo owing to the boundary between these states. Thus, enhanced surveillance and vector control of Chagas disease are highly recommended in these areas.
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Affiliation(s)
- Angélica Rosa Faria
- Laboratory of Clinical Parasitology, Pharmaceutical Sciences Faculty, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil.
| | - Juliana Barbosa Nunes
- Laboratory of Pathology of Infectious Disease, Department of Pathology, Medical School, São Paulo University, SP, Brazil
| | - Ana Laura Lara Leite
- Laboratory of Parasitology, Institute of Biomedical Sciences, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
| | - Amanda Bruno da Silva Bellini Ramos
- Laboratory of Clinical Parasitology, Pharmaceutical Sciences Faculty, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
| | - Rosângela Vieira Siqueira
- Laboratory of Clinical Parasitology, Pharmaceutical Sciences Faculty, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
| | - Ester Siqueira Caixeta Nogueira
- Department of Cell Biology and Development, Institute of Biomedical Sciences, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
| | - Marcos José Marques
- Laboratory of Parasitology, Institute of Biomedical Sciences, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
| | - Fabio Antonio Colombo
- Laboratory of Clinical Parasitology, Pharmaceutical Sciences Faculty, Universidade Federal de Alfenas, 700 Gabriel Monteiro da Silva Street, Alfenas, Minas Gerais 37130-000, Brazil
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Guerra JM, Fernandes NCCA, Réssio RA, Magno JA, Kimura LM, Barbosa JEDR, Bertollo DMB, Taniguchi HH, Hiramoto RM, Motoie G, Tolezano JE, Cogliati B. Evaluation of Cytopathological Techniques for the Diagnosis of Canine Visceral Leishmaniosis with Lymph Node Samples. J Comp Pathol 2019; 172:62-71. [PMID: 31690418 DOI: 10.1016/j.jcpa.2019.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/13/2019] [Accepted: 08/22/2019] [Indexed: 10/25/2022]
Abstract
The identification of the parasite in cytological smears of lymph node aspirates is a widely applied technique for the direct diagnosis of Leishmania spp. infection, especially in endemic areas. Although very specific, this method has limited sensitivity, and improving the technique would be highly desirable. This study aimed to evaluate the efficacy of conventional smear cytology (SC), liquid-based cytology (LBC), cell block (CB) stained with haematoxylin and eosin (HE) and immunocytochemistry (ICC), and formalin-fixed paraffin wax-embedded tissue immunohistochemistry (FFPE-IHC) compared with serology and polymerase chain reaction for the diagnosis of canine visceral leishmaniosis (CVL) in lymphoid tissue. The use of a preservative medium and centrifugation for cytological samples reduced the number of unsatisfactory artefacts/background. Moreover, LBC allowed excellent cellular preservation and the application of ancillary techniques, such as CB and ICC. SC was the most accurate morphological diagnostic method (45.0%). CB-ICC alone or associated with SC demonstrated significantly higher sensitivity (70.0% and 72.0%, respectively) when compared with SC alone (34.00%). CB-ICC was found to be more effective in the detection of infected animals with mild clinical signs, similar to FFPE-IHC. The specificity and positive predictive value were similar between all methods. Finally, the detection limit for CB-ICC and SC + CB-ICC was identical (18.46 amastigotes/mm2). Our study suggests that CB-ICC is a promising tool for improvement of the cytopathological diagnosis of CVL and may be applied in routine epidemiological screening.
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Affiliation(s)
- J M Guerra
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil; Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo, Brazil.
| | - N C C A Fernandes
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil; Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo, Brazil
| | - R A Réssio
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - J A Magno
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - L M Kimura
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - J E de R Barbosa
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - D M B Bertollo
- Centro de Laboratório Regional Instituto Adolfo Lutz São José do Rio Preto, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, Rua Alberto Sufredini Bertoni, 2325, Maceno, São José do Rio Preto, São Paulo, Brazil
| | - H H Taniguchi
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - R M Hiramoto
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - G Motoie
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - J E Tolezano
- Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria do Estado da Saúde de São Paulo, São Paulo, Brazil
| | - B Cogliati
- Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo, Brazil
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Mahfooz S, Srivastava A, Yadav MC, Tahoor A. Comparative genomics in phytopathogenic prokaryotes reveals the higher relative abundance and density of long-SSRs in the smallest prokaryotic genome. 3 Biotech 2019; 9:340. [PMID: 31478033 DOI: 10.1007/s13205-019-1872-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/13/2019] [Indexed: 10/26/2022] Open
Abstract
Frequency and distribution of long-SSRs were studied in 18 phytopathogenic prokaryotes. Higher relative abundance of the long-SSRs was observed in phytopathogenic prokaryotes when compared to non-pathogenic control. The frequency of these SSRs was positively correlated with size and GC content of the genomes of phytopathogenic prokaryotes. Interestingly, phytopathogens with higher GC content in the genome were found to posses longer repeat motifs of SSRs, whereas those having lesser GC content were harbouring shorter repeat motifs. Higher abundance of tri- and hexa-nucleotide repeat motifs were the characteristic of actinomycetes, where as higher abundance of mono- and tetra-nucleotide repeats were the characteristic of the mollicutes. The maximum relative abundance and relative density of SSR were found in the smallest genome of host-adapted pathogen Aster yellow, however, length of microsatellite repeat units was the least. On the basis of presence of SSRs in the housekeeping genes, a phylogenetic relationship between these phytopathogenic prokaryotes was deduced and compared with the phylogeny developed based on 16S ribosomal RNA gene.
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Nunes JB, Laurenti MD, Kanamura HY, Pereira AAC, Colombo FA, Marques MJ. Leishmania infantum INFECTION IN DOGS FROM THE SOUTHERN REGION OF MINAS GERAIS STATE, BRAZIL. Rev Inst Med Trop Sao Paulo 2016; 58:75. [PMID: 27828616 PMCID: PMC5096629 DOI: 10.1590/s1678-9946201658075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/13/2016] [Indexed: 11/22/2022] Open
Abstract
Visceral leishmaniasis is a systemic and chronic disease and dogs are the main reservoir of the etiologic agent, Leishmania infantum (syn L. chagasi). A serological and molecular investigation of canine visceral leishmaniasis (CVL) was performed in the municipality of Alfenas, located in the southern region of Minas Gerais, where the disease is not endemic. Samples from 87 dogs were submitted to serological tests including the Dual Path Platform (DPP(r) ) CVL Bio-Manguinhos rapid test, an in-house enzyme-linked immunosorbent assay (ELISA) and an immunofluorescence antibody test (IFAT), as well as molecular techniques such as a conventional polymerase chain reaction (PCR) with the RV1/RV2 primers and a quantitative PCR (qPCR) with the LinJ31, Ldon and DNApol primers. Of the 87 serum samples, eight (9.2%) were positive for Leishmania using the DPP rapid test, but only four (4.6%) were confirmed by ELISA and two (2.3%) by IFAT. In these two serologically confirmed cases, spleen and liver samples were positive by all the employed molecular and parasitological procedures performed on spleen samples. When whole blood samples were used in the molecular assays, two samples (2.3%) were positive only by qPCR. DNA extracted and amplified from the spleens of seropositive dogs was sequenced, showing 100% of similarity with the Leishmania infantum (syn L. chagasi) sequence. Thus, the first cases of CVL have been confirmed in the Alfenas region, suggesting the importance of canine surveys in non-endemic municipalities for CVL to monitor disease progression and to prevent outbreaks.
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Affiliation(s)
- Juliana Barbosa Nunes
- Federal University of Alfenas, Institute of Biomedical Sciences. Alfenas, MG, Brazil
| | | | | | | | - Fabio Antonio Colombo
- Federal University of Alfenas, Institute of Biomedical Sciences. Alfenas, MG, Brazil
| | - Marcos José Marques
- Federal University of Alfenas, Institute of Biomedical Sciences. Alfenas, MG, Brazil
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Chen IH, Wang JH, Chou SJ, Wu YH, Li TH, Leu MY, Chang WB, Yang WC. Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas). PeerJ 2016; 4:e1810. [PMID: 26998411 PMCID: PMC4797766 DOI: 10.7717/peerj.1810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/23/2016] [Indexed: 12/04/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct results. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from four beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have the potential to serve as an important approach to evaluating cetacean health influenced by environmental insults.
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Affiliation(s)
- I-Hua Chen
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Jiann-Hsiung Wang
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Shih-Jen Chou
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Yeong-Huey Wu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology , Pingtung , Taiwan, ROC
| | - Tsung-Hsien Li
- Department of Biology, National Museum of Marine Biology and Aquarium , Pingtung , Taiwan, ROC
| | - Ming-Yih Leu
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, ROC; Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan, ROC
| | - Wen-Been Chang
- Department of Biology, National Museum of Marine Biology and Aquarium , Pingtung , Taiwan, ROC
| | - Wei Cheng Yang
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
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7
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Selection of suitable reference genes for normalization of quantitative RT-PCR in peripheral blood samples of bottlenose dolphins (Tursiops truncatus). Sci Rep 2015; 5:15425. [PMID: 26486099 PMCID: PMC4614023 DOI: 10.1038/srep15425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/17/2015] [Indexed: 12/25/2022] Open
Abstract
Quantitative RT-PCR is often used as a research tool directed at gene transcription. Selection of optimal housekeeping genes (HKGs) as reference genes is critical to establishing sensitive and reproducible qRT-PCR-based assays. The current study was designed to identify the appropriate reference genes in blood leukocytes of bottlenose dolphins (Tursiops truncatus) for gene transcription research. Seventy-five blood samples collected from 7 bottlenose dolphins were used to analyze 15 candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ, LDHA, SDHA). HKG stability in qRT-PCR was determined using geNorm, NormFinder, BestKeeper and comparative delta Ct algorithms. Utilization of RefFinder, which combined all 4 algorithms, suggested that PGK1, HPRT1 and RPL4 were the most stable HKGs in bottlenose dolphin blood. Gene transcription perturbations in blood can serve as an indication of health status in cetaceans as it occurs prior to alterations in hematology and chemistry. This study identified HKGs that could be used in gene transcript studies, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans.
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8
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Colombo FA, Pereira-Chioccola VL, Meira CDS, Motoie G, Gava R, Hiramoto RM, de Almeida ME, da Silva AJ, Cutolo AA, Menz I. Performance of a real time PCR for leishmaniasis diagnosis using a L. (L.) infantum hypothetical protein as target in canine samples. Exp Parasitol 2015; 157:156-62. [PMID: 26297683 DOI: 10.1016/j.exppara.2015.08.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/20/2015] [Accepted: 08/16/2015] [Indexed: 10/23/2022]
Abstract
Visceral leishmaniasis represents an important public health issue in different parts of the world, requiring that measures be put in place to control the spread of the disease worldwide. The canine leishmaniasis diagnosis is not easy based on clinical signs, since dogs may not develop the infection with recognizable signs. Thus, the laboratorial diagnosis is essential to ascertain the incidence and prevalence of canine leishmaniasis especially in areas with major control efforts. Although, the diagnosis can be performed by the use of different approaches, the molecular methods such as PCR have become an indispensable tool for leishmaniases diagnosis. A TaqMan assay for real-time PCR (Linj31-qPCR) was developed to determine the parasite occurrence in clinical cases of leishmaniasis. The assay targets an L. (L.) infantum hypothetical protein region. The specificity of the assay was verified by using Leishmania World Health Organization reference strains including parasites belonging to subgenus L. (Leishmania), subgenus L. (Viannia), other Leishmania species and Trypanosoma cruzi. The sensitivity was verified by using isolates of L. (L.) amazonensis and L. (L.) infantum. The usefulness of the assay for diagnosis was ascertained by testing 277 samples from dogs in regions endemic for visceral and/or cutaneous leishmaniasis and from regions in which leishmaniasis was not endemic in São Paulo State, Brazil. Diagnosis of canine visceral leishmaniasis (CVL) was determined on these animals by conventional PCR and three serological tests. The dog samples were divided into four groups. I, dogs with CVL (n = 101); II, dogs with other diseases and without CVL (n = 97); III, dogs with American cutaneous leishmaniasis (n = 7), and, IV, dogs without CVL (n = 72) from areas where leishmaniasis was not endemic as control group. Results indicated that Linj31-qPCR was able to identify parasites belonging to subgenus L. (Leishmania) with no cross-amplification with other parasite subgenera. The Linj31-qPCR detected Leishmania parasites DNA in 98% of samples from Group I. In conclusion this methodology can be used as routine diagnostic tools to detect parasites from subgenus Leishmania.
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Affiliation(s)
- Fabio Antonio Colombo
- Laboratório de Biologia Molecular de Micro-organismos da Universidade Federal de Alfenas, Alfenas, MG, Brazil
| | - Vera Lucia Pereira-Chioccola
- Laboratorio de Biologia Molecular de Parasitas, Centro de Parasitologia e Micologia do Instituto Adolfo Lutz, Sao Paulo, SP, Brazil.
| | - Cristina da Silva Meira
- Laboratorio de Biologia Molecular de Parasitas, Centro de Parasitologia e Micologia do Instituto Adolfo Lutz, Sao Paulo, SP, Brazil
| | - Gabriela Motoie
- Laboratorio de Biologia Molecular de Parasitas, Centro de Parasitologia e Micologia do Instituto Adolfo Lutz, Sao Paulo, SP, Brazil
| | - Ricardo Gava
- Laboratorio de Biologia Molecular de Parasitas, Centro de Parasitologia e Micologia do Instituto Adolfo Lutz, Sao Paulo, SP, Brazil
| | - Roberto M Hiramoto
- Nucleo de Parasitoses Sistemicas, Centro de Parasitologia e Micologia do Instituto Adolfo Lutz, Sao Paulo, SP, Brazil
| | - Marcos E de Almeida
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Public Health Service, Atlanta, GA, USA
| | - Alexandre J da Silva
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Public Health Service, Atlanta, GA, USA
| | - Andre Antonio Cutolo
- Setor de Controle de Zoonoses e Vetores, Prefeitura Municipal de Monte Mor, Monte Mor, SP, Brazil
| | - Ingrid Menz
- Ingrid Menz Micro Empresa, Campinas, SP, Brazil
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Wen J, Zhang Y, Yau SS. k-mer Sparse matrix model for genetic sequence and its applications in sequence comparison. J Theor Biol 2014; 363:145-50. [DOI: 10.1016/j.jtbi.2014.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 07/14/2014] [Accepted: 08/17/2014] [Indexed: 10/24/2022]
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Castro-Júnior JG, Freire ML, Campos SPS, Scopel KKG, Porrozzi R, Da Silva ED, Colombo FA, da Silveira RDCV, Marques MJ, Coimbra ES. Evidence of Leishmania (Leishmania) infantum infection in dogs from Juiz de Fora, Minas Gerais State, Brazil, based on immunochromatographic dual-path platform (DPP®) and PCR assays. Rev Inst Med Trop Sao Paulo 2014; 56:225-9. [PMID: 24879001 PMCID: PMC4085865 DOI: 10.1590/s0036-46652014000300008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/24/2013] [Indexed: 11/23/2022] Open
Abstract
In Brazil, domestic dogs are branded as the primary reservoir for zoonotic
visceral leishmaniasis, due to the clear positive correlation observed between human
and canine infection rates. This study aimed to carry out a serological survey of
canine visceral leishmaniasis (CVL) in dogs housed at a public kennel in the
municipality of Juiz de Fora, Minas Gerais State, Brazil, using the
immunochromatographic TR DPP® CVL rapid test. Additionally, conventional
and/or real time PCR assay was used to detect and confirm L.
infantum infection in the DPP positive dogs only. Of the 400 dogs
studied, most did not present clinical signs for CVL (p < 0.05),
and fifteen (3.8%) were seropositive in the DPP test. There was no statistically
significant difference between the DPP seropositive dogs and the clinical signs of
the disease (p > 0.05). Both conventional and real time PCR tests
confirmed L. infantum infection in nine (75.0%) of the twelve DPP
seropositive dogs that remained alive during the follow-up period. This study is the
first seroepidemiologic survey of CVL held in the city of Juiz de Fora, and the
results reinforce the idea that this disease is currently in a process of expansion
and urbanization in Brazil. Furthermore, this study highlights the use of the DPP
test as an alternative for diagnosing CVL in large and mid-sized cities, due to its
ease of implementation.
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Affiliation(s)
- José Geraldo Castro-Júnior
- Programa de Pós-graduação em Saúde Brasileira, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Mariana Lourenço Freire
- Departamento de Parasitologia, Microbiologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Samantha Priscila Silva Campos
- Departamento de Parasitologia, Microbiologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Kezia K G Scopel
- Departamento de Parasitologia, Microbiologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Renato Porrozzi
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Fabio A Colombo
- Laboratório de Parasitologia, Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Rita de Cássia Viveiros da Silveira
- Laboratório de Parasitologia, Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Marcos José Marques
- Laboratório de Parasitologia, Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Elaine Soares Coimbra
- Departamento de Parasitologia, Microbiologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
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11
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Evaluation of PCR in the diagnosis of canine leishmaniasis in two different epidemiological regions: Campinas (SP) and Teresina (PI), Brazil. Epidemiol Infect 2014; 143:1088-95. [DOI: 10.1017/s0950268814001721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYUsing the polymerase chain reaction (PCR) test for diagnosis of canine leishmaniasis has greater sensitivity and specificity than culture and visualization of the parasite. This study compares PCR for the diagnosis of the genus and species ofLeishmaniawith serological techniques used for the control of canine visceral leishmaniasis (CVL) in Brazil, considering two regions. We analysed peripheral blood samples collected from 195 dogs in the Campinas (SP) and Teresina (PI) regions. ELISA was performed as a serological method and PCR was performed using specific primers for the genusLeishmaniaspp. and the speciesLeishmania chagasi. In Campinas, a greater sensitivity of PCR (88·24%) (P = 0·0455) compared to Teresina (14·71%) (P < 0·0001) was observed, and an agreement was observed for Cohen's kappa index (0·9096). Both PCR and ELISA showed discordance for sensitivity (Campinas 100%, Teresina 21·74%), specificity (Campinas 30·77%, Teresina 100%), positive predictive value (Campinas 68·97%, Teresina 100%), negative predictive value (Campinas 100%, Teresina 37·94%) and Cohen's kappa index (0·1238). This study confirms the importance of PCR in analysis of the canine reservoir, and as an effective method for the detection of active and recent infection.
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K-mer natural vector and its application to the phylogenetic analysis of genetic sequences. Gene 2014; 546:25-34. [PMID: 24858075 DOI: 10.1016/j.gene.2014.05.043] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/04/2014] [Accepted: 05/20/2014] [Indexed: 11/21/2022]
Abstract
Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.
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Gowane GR, Sharma AK, Sankar M, Narayanan K, Bisht P, Subramaniam S, Pattnaik B. The expression of IL6 and 21 in crossbred calves upregulated by inactivated trivalent FMD vaccine. Anim Biotechnol 2014; 25:108-18. [PMID: 24555796 DOI: 10.1080/10495398.2013.834826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Foot and mouth disease (FMD) is an economically important disease and a whole-virus inactivated trivalent virus vaccine is the mainstay for controlling the disease in India. The protective humoral immune response to FMD vaccination is a complex, but, tightly regulated process mediated by the interplay of interleukins (IL). Based on the specific role of IL6 and 21 in adaptive immune response, we hypothesized that inactivated trivalent FMD vaccine would stimulate IL6 and 21 expression in the circulating lymphocytes. The expressions of IL6 and 21 were assayed on 0, 28, 60, 90, and 120 d post-vaccination (DPV) by quantitative PCR (qPCR) with simultaneous assessment of FMDV antibody titer by liquid phase blocking ELISA. The results revealed that the peak expression of IL6 and 21 was on DPV 28 which correlated well with the FMDV antibody titer and plummeted to the prevaccination titer level by 60 DPV. As IL21 is the final effector of antibody production as compared to IL6, we investigated the expression of IL21 in calves that had protective titer (>1.8) with the unprotected group (<1.8). Expression of IL21 on 28 DPV was numerically higher in the protected than that of the unprotected group of calves.
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Affiliation(s)
- G R Gowane
- a Central Sheep & Wool Research Institute , Avikanagar , Rajasthan , India
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Hu JY, Zhang YP, Yu L. Summary of Laurasiatheria (mammalia) phylogeny. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2013; 33:E65-74. [PMID: 23266984 DOI: 10.3724/sp.j.1141.2012.e05-06e65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.
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15
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GAPDH Pseudogenes and the Quantification of Feline Genomic DNA Equivalents. Mol Biol Int 2013; 2013:587680. [PMID: 23738070 PMCID: PMC3655645 DOI: 10.1155/2013/587680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/21/2013] [Accepted: 03/28/2013] [Indexed: 01/14/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is broadly used to detect and quantify nucleic acid targets. In order to determine cell copy number and genome equivalents, a suitable reference gene that is present in a defined number in the genome is needed, preferably as a single copy gene. For most organisms, a variable number of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) pseudogenes have been reported. However, it has been suggested that a single-copy of the GAPDH pseudogene is present in the feline genome and that a GAPDH assay can therefore be used to quantify feline genomic DNA (gDNA). The aim of this study was to determine whether one or more GAPDH pseudogenes are present in the feline genome and to provide a suitable alternative qPCR system for the quantification of feline cell copy number and genome equivalents. Bioinformatics and sequencing results revealed that not just one but several closely related GAPDH-like sequences were present in the cat genome. We thus identified, developed, optimized, and validated an alternative reference gene assay using feline albumin (fALB). Our data emphasize the need for an alternative reference gene, apart from the GAPDH pseudogene, for the normalization of gDNA levels. We recommend using the fALB qPCR assay for future studies.
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Bischoff SR, Tsai SQ, Hardison NE, Motsinger-Reif AA, Freking BA, Nonneman DJ, Rohrer GA, Piedrahita JA. Differences in X-chromosome transcriptional activity and cholesterol metabolism between placentae from swine breeds from Asian and Western origins. PLoS One 2013; 8:e55345. [PMID: 23383161 PMCID: PMC3561265 DOI: 10.1371/journal.pone.0055345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/21/2012] [Indexed: 12/19/2022] Open
Abstract
To gain insight into differences in placental physiology between two swine breeds noted for their dissimilar reproductive performance, that is, the Chinese Meishan and white composite (WC), we examined gene expression profiles of placental tissues collected at 25, 45, 65, 85, and 105 days of gestation by microarrays. Using a linear mixed model, a total of 1,595 differentially expressed genes were identified between the two pig breeds using a false-discovery rate q-value ≤0.05. Among these genes, we identified breed-specific isoforms of XIST, a long non-coding RNA responsible X-chromosome dosage compensation in females. Additionally, we explored the interaction of placental gene expression and chromosomal location by DIGMAP and identified three Sus scrofa X chromosomal bands (Xq13, Xq21, Xp11) that represent transcriptionally active clusters that differ between Meishan and WC during placental development. Also, pathway analysis identified fundamental breed differences in placental cholesterol trafficking and its synthesis. Direct measurement of cholesterol confirmed that the cholesterol content was significantly higher in the Meishan versus WC placentae. Taken together, this work identifies key metabolic pathways that differ in the placentae of two swine breeds noted for differences in reproductive prolificacy.
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Affiliation(s)
- Steve R. Bischoff
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Shengdar Q. Tsai
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Nicholas E. Hardison
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison A. Motsinger-Reif
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bradley A. Freking
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Dan J. Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Gary A. Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Moura AE, Natoli A, Rogan E, Hoelzel AR. Evolution of Functional Genes in Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level. Evol Biol 2012. [DOI: 10.1007/s11692-012-9215-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Luo H, Arndt W, Zhang Y, Shi G, Alekseyev M, Tang J, Hughes AL, Friedman R. Phylogenetic analysis of genome rearrangements among five mammalian orders. Mol Phylogenet Evol 2012; 65:871-82. [PMID: 22929217 PMCID: PMC4425404 DOI: 10.1016/j.ympev.2012.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 08/11/2012] [Accepted: 08/13/2012] [Indexed: 01/16/2023]
Abstract
Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.
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Affiliation(s)
- Haiwei Luo
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - William Arndt
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Yiwei Zhang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Guanqun Shi
- Department of Computer Science, University of California, Riverside, 92521, USA
| | - Max Alekseyev
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - Robert Friedman
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
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Expression of NADPH oxidase (NOX) 5 in rabbit corneal stromal cells. PLoS One 2012; 7:e34440. [PMID: 22511941 PMCID: PMC3325249 DOI: 10.1371/journal.pone.0034440] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 03/02/2012] [Indexed: 01/10/2023] Open
Abstract
Purpose To determine whether NOX 5 is expressed in rabbit corneal stromal cells (RCSC). NADPH oxidases (NOXes) are enzymes that preferentially use NADPH as a substrate and generate superoxide. Several isoforms of NOXes function as multi-protein complexes while NOX5 and DUOXs do not require the accessory proteins for their activity and possess calcium binding EF hands. Methods Human NOX5 primers were used to amplify the rabbit NOX5 by RT-PCR. Amplified product was sequenced to confirm its identity. The protein encoded by the NOX5 was identified by western blot analysis. NOX5 siRNA was used to reduce transcript, protein, and calcium stimulated activity. In silico analyses were performed to establish the putative structure, functions, and evolution of rabbit NOX5. Results NOX activity was measured in RCSC with NADPH rather than NADH as a substrate. RT-PCR with NOX5 primers amplified 288 bp product using RCSC cDNA, which, when sequenced, confirmed its identity to human NOX5 mRNA. This sequence was used to predict the rabbit (Oryctolagus cuniculus) NOX5 gene. NOX5 siRNA reduced amounts of NOX5 mRNA in RCSC and reduced ionomycin stimulated superoxide production. A protein of about 65 to 70 kDa encoded by the NOX5 was detected by western blot analysis. In silico analysis predicted a putative rabbit NOX5 protein containing 801 amino acids. Motif searches predicted the presence of at least 3 putative EF-hands in N-terminus and a NOX domain in C terminal region. Conclusions The data document that the NOX5 gene was expressed in cells of lagomorphs unlike rodents, making the rabbit an interesting model to study NOX5 functions. The activity of the rabbit NOX5 was calcium stimulated, a trait of NOX5 in general. NOX5 may also prove to be a useful genetic marker for studying the taxonomic position of lagomorphs and the Glires classification.
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20
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Zhou X, Xu S, Xu J, Chen B, Zhou K, Yang G. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals. Syst Biol 2012; 61:150-64. [PMID: 21900649 PMCID: PMC3243735 DOI: 10.1093/sysbio/syr089] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 04/06/2011] [Accepted: 06/23/2011] [Indexed: 11/24/2022] Open
Abstract
Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Junxiao Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Bingyao Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Herculano-Houzel S, Ribeiro P, Campos L, Valotta da Silva A, Torres LB, Catania KC, Kaas JH. Updated neuronal scaling rules for the brains of Glires (rodents/lagomorphs). BRAIN, BEHAVIOR AND EVOLUTION 2011; 78:302-14. [PMID: 21985803 DOI: 10.1159/000330825] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 07/07/2011] [Indexed: 11/19/2022]
Abstract
Brain size scales as different functions of its number of neurons across mammalian orders such as rodents, primates, and insectivores. In rodents, we have previously shown that, across a sample of 6 species, from mouse to capybara, the cerebral cortex, cerebellum and the remaining brain structures increase in size faster than they gain neurons, with an accompanying decrease in neuronal density in these structures [Herculano-Houzel et al.: Proc Natl Acad Sci USA 2006;103:12138-12143]. Important remaining questions are whether such neuronal scaling rules within an order apply equally to all pertaining species, and whether they extend to closely related taxa. Here, we examine whether 4 other species of Rodentia, as well as the closely related rabbit (Lagomorpha), conform to the scaling rules identified previously for rodents. We report the updated neuronal scaling rules obtained for the average values of each species in a way that is directly comparable to the scaling rules that apply to primates [Gabi et al.: Brain Behav Evol 2010;76:32-44], and examine whether the scaling relationships are affected when phylogenetic relatedness in the dataset is accounted for. We have found that the brains of the spiny rat, squirrel, prairie dog and rabbit conform to the neuronal scaling rules that apply to the previous sample of rodents. The conformity to the previous rules of the new set of species, which includes the rabbit, suggests that the cellular scaling rules we have identified apply to rodents in general, and probably to Glires as a whole (rodents/lagomorphs), with one notable exception: the naked mole-rat brain is apparently an outlier, with only about half of the neurons expected from its brain size in its cerebral cortex and cerebellum.
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Affiliation(s)
- Suzana Herculano-Houzel
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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22
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Deng M, Yu C, Liang Q, He RL, Yau SST. A novel method of characterizing genetic sequences: genome space with biological distance and applications. PLoS One 2011; 6:e17293. [PMID: 21399690 PMCID: PMC3047556 DOI: 10.1371/journal.pone.0017293] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/28/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences. METHODOLOGY To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses. CONCLUSIONS Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve.
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Affiliation(s)
- Mo Deng
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Chenglong Yu
- The Institute of Mathematical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Qian Liang
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Rong L. He
- Department of Biological Sciences, Chicago State University, Chicago, Illinois, United States of America
| | - Stephen S.-T. Yau
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Colombo FA, Odorizzi RMFN, Laurenti MD, Galati EAB, Canavez F, Pereira-Chioccola VL. Detection of Leishmania (Leishmania) infantum RNA in fleas and ticks collected from naturally infected dogs. Parasitol Res 2011; 109:267-74. [DOI: 10.1007/s00436-010-2247-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 12/24/2010] [Indexed: 10/18/2022]
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Poulakakis N, Stamatakis A. Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history. SYST BIODIVERS 2010. [DOI: 10.1080/14772000.2010.484436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci U S A 2010; 107:4629-34. [PMID: 20176949 DOI: 10.1073/pnas.0910915107] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modeling the interplay between mutation and selection at the molecular level is key to evolutionary studies. To this end, codon-based evolutionary models have been proposed as pertinent means of studying long-range evolutionary patterns and are widely used. However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized. Here, we integrate recent developments in nonparametric statistical approaches to propose a probabilistic model that accounts for the heterogeneity of amino acid fitness profiles across the coding positions of a gene. We apply the model to a dozen real protein-coding gene alignments and find it to produce biologically plausible inferences, for instance, as pertaining to site-specific amino acid constraints, as well as distributions of scaled selection coefficients. In their account of mutational features as well as the heterogeneous regimes of selection at the amino acid level, the modeling approaches studied here can form a backdrop for several extensions, accounting for other selective features, for variable population size, or for subtleties of mutational features, all with parameterizations couched within population-genetic theory.
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Asher RJ, Bennett N, Lehmann T. The new framework for understanding placental mammal evolution. Bioessays 2010; 31:853-64. [PMID: 19582725 DOI: 10.1002/bies.200900053] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub-clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, University of Cambridge, Downing St., Cambridge CB23EJ, UK.
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Kato A, Rooney AP, Furutani Y, Hirose S. Evolution of trappin genes in mammals. BMC Evol Biol 2010; 10:31. [PMID: 20113469 PMCID: PMC2831891 DOI: 10.1186/1471-2148-10-31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 01/29/2010] [Indexed: 01/10/2023] Open
Abstract
Background Trappin is a multifunctional host-defense peptide that has antiproteolytic, antiinflammatory, and antimicrobial activities. The numbers and compositions of trappin paralogs vary among mammalian species: human and sheep have a single trappin-2 gene; mouse and rat have no trappin gene; pig and cow have multiple trappin genes; and guinea pig has a trappin gene and two other derivativegenes. Independent duplications of trappin genes in pig and cow were observed recently after the species were separated. To determine whether these trappin gene duplications are restricted only to certain mammalian lineages, we analyzed recently-developed genome databases for the presence of duplicate trappin genes. Results The database analyses revealed that: 1) duplicated trappin multigenes were found recently in the nine-banded armadillo; 2) duplicated two trappin genes had been found in the Afrotherian species (elephant, tenrec, and hyrax) since ancient days; 3) a single trappin-2 gene was found in various eutherians species; and 4) no typical trappin gene has been found in chicken, zebra finch, and opossum. Bayesian analysis estimated the date of the duplication of trappin genes in the Afrotheria, guinea pig, armadillo, cow, and pig to be 244, 35, 11, 13, and 3 million-years ago, respectively. The coding regions of trappin multigenes of almadillo, bovine, and pig evolved much faster than the noncoding exons, introns, and the flanking regions, showing that these genes have undergone accelerated evolution, and positive Darwinian selection was observed in pig-specific trappin paralogs. Conclusion These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes.
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Affiliation(s)
- Akira Kato
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
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Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A 2009; 106:17077-82. [PMID: 19805074 DOI: 10.1073/pnas.0909377106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten complete mammalian genome sequences were compared by using the "feature frequency profile" (FFP) method of alignment-free comparison. This comparison technique reveals that the whole nongenic portion of mammalian genomes contains evolutionary information that is similar to their genic counterparts--the intron and exon regions. We partitioned the complete genomes of mammals (such as human, chimp, horse, and mouse) into their constituent nongenic, intronic, and exonic components. Phylogenic species trees were constructed for each individual component class of genome sequence data as well as the whole genomes by using standard tree-building algorithms with FFP distances. The phylogenies of the whole genomes and each of the component classes (exonic, intronic, and nongenic regions) have similar topologies, within the optimal feature length range, and all agree well with the evolutionary phylogeny based on a recent large dataset, multispecies, and multigene-based alignment. In the strictest sense, the FFP-based trees are genome phylogenies, not species phylogenies. However, the species phylogeny is highly related to the whole-genome phylogeny. Furthermore, our results reveal that the footprints of evolutionary history are spread throughout the entire length of the whole genome of an organism and are not limited to genes, introns, or short, highly conserved, nongenic sequences that can be adversely affected by factors (such as a choice of sequences, homoplasy, and different mutation rates) resulting in inconsistent species phylogenies.
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Bischoff SR, Tsai S, Hardison N, Motsinger-Reif AA, Freking BA, Nonneman D, Rohrer G, Piedrahita JA. Characterization of conserved and nonconserved imprinted genes in swine. Biol Reprod 2009; 81:906-20. [PMID: 19571260 DOI: 10.1095/biolreprod.109.078139] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To increase our understanding of imprinted genes in swine, we carried out a comprehensive analysis of this gene family using two complementary approaches: expression and phenotypic profiling of parthenogenetic fetuses, and analysis of imprinting by pyrosequencing. The parthenote placenta and fetus were smaller than those of controls but had no obvious morphological differences at Day 28 of gestation. By Day 30, however, the parthenote placentas had decreased chorioallantoic folding, decreased chorionic ruggae, and reduction of fetal-maternal interface surface in comparison with stage-matched control fetuses. Using Affymetrix Porcine GeneChip microarrays and/or semiquantitative PCR, brain, fibroblast, liver, and placenta of Day 30 fetuses were profiled, and 25 imprinted genes were identified as differentially expressed in at least one of the four tissue types: AMPD3, CDKN1C, COPG2, DHCR7, DIRAS3, IGF2 (isoform specific), IGF2AS, IGF2R, MEG3, MEST, NAP1L5, NDN, NNAT, OSBPL1A, PEG3, APEG3, PEG10, PLAGL1, PON2, PPP1R9A, SGCE, SLC38A4, SNORD107, SNRPN, and TFPI2. For DIRAS3, PLAGL1, SGCE, and SLC38A4, tissue-specific differences were detected. In addition, we examined the imprinting status of candidate genes by quantitative allelic pyrosequencing. Samples were collected from Day 30 pregnancies generated from reciprocal crosses of Meishan and White Composite breeds, and single-nucleotide polymorphisms were identified in candidate genes. Imprinting was confirmed for DIRAS3, DLK1, H19, IGF2AS, NNAT, MEST, PEG10, PHLDA2, PLAGL1, SGCE, and SNORD107. We also found no evidence of imprinting in ASB4, ASCL2, CD81, COMMD1, DCN, DLX5, and H13. Combined, these results represent the most comprehensive survey of imprinted genes in swine to date.
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Affiliation(s)
- Steve R Bischoff
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina 27606, USA
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Hou ZC, Romero R, Wildman DE. Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data. Mol Phylogenet Evol 2009; 52:660-4. [PMID: 19435603 DOI: 10.1016/j.ympev.2009.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 04/17/2009] [Accepted: 05/04/2009] [Indexed: 11/17/2022]
Abstract
Great progress has been made toward resolving the evolutionary relationships among extant mammals, yet there are still areas of disagreement. The relationships among ferungulates that have high quality draft genome sequences available (i.e. dog, cow, horse) are unresolved, and thus we examined their phylogeny using currently known mammalian 1:1 orthologs. This dataset consists of 40 million base pairs from 2705 protein-coding genes. Maximum likelihood and Bayesian analyses of the combined and individual gene phylogenies strongly support a sister grouping of cow and horse to the exclusion of dog although topology tests could not rule out a horse and dog sister group relationship.
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Affiliation(s)
- Zhuo-Cheng Hou
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development/NIH/DHHS, Detroit, MI 48201, USA
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31
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Schneider A, Cannarozzi GM. Support patterns from different outgroups provide a strong phylogenetic signal. Mol Biol Evol 2009; 26:1259-72. [PMID: 19240194 DOI: 10.1093/molbev/msp034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade.
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Affiliation(s)
- Adrian Schneider
- ETH Zurich, Department of Computer Science, Zurich, Switzerland.
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Huang X, Li Y, Zheng CY. A novel single-cell quantitative real-time RT-PCR method for quantifying foot-and-mouth disease viral RNA. J Virol Methods 2008; 155:150-6. [PMID: 19010355 DOI: 10.1016/j.jviromet.2008.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 09/26/2008] [Accepted: 10/02/2008] [Indexed: 10/21/2022]
Abstract
Foot-and-mouth disease virus is a positive-sense, single-stranded RNA virus with a negative strand as its replication intermediate, which can cause severe acute infection in sensitive cell lines. To investigate better the actual state of virus infection, there is a need to measure the amount of FMDV RNA in a single acutely infected cell rather than in a large number of cells. Therefore, in the present study, a strand-specific single-cell quantitative real-time RT-PCR was developed to analyze the RNA or FMDV. This new method uses two techniques in concert with each other: a technique for isolating single cells with micromanipulators, which is coupled to an assay for detecting viral RNA by real-time RT-PCR. In the assay of acute infection, 185 of 224 (82.6%) single-cell samples were positive and contained viral genome copies ranging from several to thousands, and up to 1,000,000 copies. However, not all cells were infected and there were differences in the number of viral RNA copies between cells. A single-cell quantitative RT-PCR was validated to be feasible and effective.
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Affiliation(s)
- Xuan Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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33
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Asher RJ, Geisler JH, Sánchez-Villagra MR. Morphology, paleontology, and placental mammal phylogeny. Syst Biol 2008; 57:311-7. [PMID: 18432551 DOI: 10.1080/10635150802033022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Robert J Asher
- Department of Zoology, University of Cambridge, Downing Street, UK
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Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. The human phylome. Genome Biol 2008; 8:R109. [PMID: 17567924 PMCID: PMC2394744 DOI: 10.1186/gb-2007-8-6-r109] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 03/16/2007] [Accepted: 06/13/2007] [Indexed: 01/09/2023] Open
Abstract
The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed. Background: Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them. Results: We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes. Conclusion: Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.
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Affiliation(s)
- Jaime Huerta-Cepas
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain
| | - Hernán Dopazo
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain
| | - Joaquín Dopazo
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain
| | - Toni Gabaldón
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain
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Abstract
Recent progress resolving the phylogenetic relationships of the major lineages of mammals has had a broad impact in evolutionary biology, comparative genomics and the biomedical sciences. Novel insights into the timing and historical biogeography of early mammalian diversification have resulted from a new molecular tree for placental mammals coupled with dating approaches that relax the assumption of the molecular clock. We highlight the numerous applications to come from a well-resolved phylogeny and genomic prospecting in multiple lineages of mammals, from identifying regulatory elements in mammalian genomes to assessing the functional consequences of mutations in human disease loci and those driving adaptive evolution.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Wildman DE, Uddin M, Opazo JC, Liu G, Lefort V, Guindon S, Gascuel O, Grossman LI, Romero R, Goodman M. Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci U S A 2007; 104:14395-400. [PMID: 17728403 PMCID: PMC1958817 DOI: 10.1073/pnas.0704342104] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Indexed: 11/18/2022] Open
Abstract
Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively resolved the basal branching order within Placentalia. Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of crown placental mammals. Focusing on approximately 1,700 conserved gene loci, those that have the more slowly evolving coding sequences, and using maximum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree reconstruction methods, we find from almost all results that a clade (the southern Atlantogenata) composed of Afrotheria and Xenarthra is the sister group of all other (the northern Boreoeutheria) crown placental mammals, among boreoeutherians Rodentia groups with Lagomorpha, and the resultant Glires is close to Primates. Only the NJ tree for nucleotide sequences separates Rodentia (murids) first and then Lagomorpha (rabbit) from the other placental mammals. However, this nucleotide NJ tree still depicts Atlantogenata and Boreoeutheria but minus Rodentia and Lagomorpha. Moreover, the NJ tree for amino acid sequences does depict the basal separation to be between Atlantogenata and a Boreoeutheria that includes Rodentia and Lagomorpha. Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.
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Affiliation(s)
- Derek E. Wildman
- Perinatology Research Branch, National Institute of Child Health and Human Development/National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
- Center For Molecular Medicine and Genetics, and
- Departments of Obstetrics and Gynecology and
| | | | - Juan C. Opazo
- Center For Molecular Medicine and Genetics, and
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588; and
| | - Guozhen Liu
- Center For Molecular Medicine and Genetics, and
| | - Vincent Lefort
- Laboratory of Computer Science, Robotics, and Microelectronics, Centre National de la Recherche Scientifique, Université Montpellier II, 161 Rue Ada, 34392 Montpellier, France
| | - Stephane Guindon
- Laboratory of Computer Science, Robotics, and Microelectronics, Centre National de la Recherche Scientifique, Université Montpellier II, 161 Rue Ada, 34392 Montpellier, France
| | - Olivier Gascuel
- Laboratory of Computer Science, Robotics, and Microelectronics, Centre National de la Recherche Scientifique, Université Montpellier II, 161 Rue Ada, 34392 Montpellier, France
| | | | - Roberto Romero
- Perinatology Research Branch, National Institute of Child Health and Human Development/National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Morris Goodman
- Center For Molecular Medicine and Genetics, and
- Anatomy and Cell Biology, Wayne State University, Detroit, MI 48201
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Kullberg M, Hallström B, Arnason U, Janke A. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution. PLoS One 2007; 2:e775. [PMID: 17712423 PMCID: PMC1942079 DOI: 10.1371/journal.pone.0000775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 07/24/2007] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant). METHODOLOGY/PRINCIPAL FINDINGS We have produced 2000 ESTs (1.2 mega bases) from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.
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Affiliation(s)
- Morgan Kullberg
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden.
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38
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Niimura Y, Nei M. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2007; 2:e708. [PMID: 17684554 PMCID: PMC1933591 DOI: 10.1371/journal.pone.0000708] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/04/2007] [Indexed: 11/25/2022] Open
Abstract
Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800–1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression.
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Affiliation(s)
- Yoshihito Niimura
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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Hallström BM, Kullberg M, Nilsson MA, Janke A. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol Biol Evol 2007; 24:2059-68. [PMID: 17630282 DOI: 10.1093/molbev/msm136] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The phylogenetic positions of the 4 clades, Euarchontoglires, Laurasiatheria, Afrotheria, and Xenarthra, have been major issues in the recent discussion of basal relationships among placental mammals. However, despite considerable efforts these relationships, crucial to the understanding of eutherian evolution and biogeography, have remained essentially unresolved. Euarchontoglires and Laurasiatheria are generally joined into a common clade (Boreoeutheria), whereas the position of Afrotheria and Xenarthra relative to Boreoeutheria has been equivocal in spite of the use of comprehensive amounts of nuclear encoded sequences or the application of genome-level characters such as retroposons. The probable reason for this uncertainty is that the divergences took place long time ago and within a narrow temporal window, leaving only short common branches. With the aim of further examining basal eutherian relationships, we have collected conserved protein-coding sequences from 11 placental mammals, a marsupial and a bird, whose nuclear genomes have been largely sequenced. The length of the alignment of homologous sequences representing each individual species is 2,168,859 nt. This number of sites, representing 2840 protein-coding genes, exceeds by a considerable margin that of any previous study. The phylogenetic analysis joined Xenarthra and Afrotheria on a common branch, Atlantogenata. This topology was found to fit the data significantly better than the alternative trees.
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Affiliation(s)
- Björn M Hallström
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden
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40
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Asher RJ. A web-database of mammalian morphology and a reanalysis of placental phylogeny. BMC Evol Biol 2007; 7:108. [PMID: 17608930 PMCID: PMC1941728 DOI: 10.1186/1471-2148-7-108] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 07/03/2007] [Indexed: 11/26/2022] Open
Abstract
Background Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny. Results The results reinforce the growing consensus regarding the extant placental mammal clades of Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel) characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria. Bayesian analyses of morphology, indels, and DNA support both a basal position for Afrotheria and the position of Cretaceous eutherians outside of crown Placentalia. Depending on treatment of third codon positions, the affinity of several fossils (Leptictis,Paleoparadoxia, Plesiorycteropus and Zalambdalestes) vary, highlighting the potential effect of sequence data on fossils for which such data are missing. Conclusion The combined dataset supports the location of the placental mammal root at Afrotheria or Xenarthra, not at Erinaceus or rodents. Even a small morphological dataset can have a marked influence on the location of the root in a combined-data analysis. Additional morphological data are desirable to better reconstruct the position of several fossil taxa; and the graphic-rich, web-based morphology data matrix presented here will make it easier to incorporate more taxa into a larger data matrix.
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Affiliation(s)
- Robert J Asher
- Museum of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Huttley GA, Wakefield MJ, Easteal S. Rates of genome evolution and branching order from whole genome analysis. Mol Biol Evol 2007; 24:1722-30. [PMID: 17494028 DOI: 10.1093/molbev/msm094] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences.
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Affiliation(s)
- Gavin A Huttley
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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Chromosome painting in the manatee supports Afrotheria and Paenungulata. BMC Evol Biol 2007; 7:6. [PMID: 17244368 PMCID: PMC1784077 DOI: 10.1186/1471-2148-7-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 01/23/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee. RESULTS The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19. CONCLUSION There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking afrotherian taxa.
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