Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae)

MacEachern, Sean; McEwan, John C.; Goddard, Michael E.

doi:10.1186/1471-2164-10-177

Cited by 62 publications

(77 citation statements)

References 48 publications

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“…They found that cows are classified in genus Bos, goats in genus Capra, while buffaloes (both Syncerus caffer and Bubalus bubalis) in genus Bubalus. A similar finding was also stated by MacEachern et al (2009) who conducted species phylogeny reconstruction under the cluster of Bovini, who found that species from genus Bubalus and Syncerus are under the same cluster of buffaloes.…”

Section: The Composition Of Nucleotide and Variable Regionsupporting

confidence: 64%

Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

Sukri¹,

Amin

Winaya

et al. 2015

BIOMEDNATPROCH

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This research aims to investigate the substitution pattern of nucleotide base and haplotype diversity of Indonesian swamp buffalo (Bubalus bubalis) based on the mitochondrial DNA cyt b partial gene sequence. 17 samples were chosen from 7 different regions with each uniquely represents Indonesian biogeography which comprise Aceh, Riau, Madiun, Blitar, Lombok, South Borneo and Tana Toraja. The result of cyt b gene sequence alignment showed the presence of transition and transversion substitutions and the absence of insertion and deletion. The amount of transitions was found to be higher than that of transversions and the amount of substitution in pyrimidine was also higher than that in purine. The highest amount of transitions happened in base TC which is a silent substitution. The result of median joining network analysis showed that Indonesian haplotype Bubalus bubalis could be classified into 16 haplotypes which form different haplogroups unique to their geographical region. The result of median joining network analysis also indicated that the genetic relationships of swamp buffaloes (Bubalus bubalis) in Indonesia are highly influenced by their geographical locations.

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Section: The Composition Of Nucleotide and Variable Regionsupporting

confidence: 64%

Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

Sukri¹,

Amin

Winaya

et al. 2015

BIOMEDNATPROCH

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“…Although mtDNA amounts do not change during in vivo preimplantation development (Kameyama et al, 2007;Pikó and Taylor, 1987;Smith et al, 2005;Steinborn et al, 1998), embryos cultured in vitro often show increased mtDNA amounts between zygote and blastocyst stages in a number of species (Chiaratti et al, 2010;Kameyama et al, 2007;May-Panloup et al, 2005;McConnell and Petrie, 2004;Mtango et al, 2008;Smith et al, 2005;Spikings et al, 2007) including after iSCNT within the Bos genus, for example, B. gaurus and B. taurus (Mastromonaco et al, 2007). Nonetheless, although variations in embryo in vitro culture systems may account for part of the differences in mtDNA levels (Kameyama et al, 2007;McConnell and Petrie, 2004;Mtango et al, 2008), complete lack of amplification of donor mtDNA in these XOT embryos during in vitro development may further reflect the nuclearmitochondrial incompatibilities (Bowles et al, 2008;Gó mez et al, 2009;Kenyon and Moraes, 1997;Lanza et al, 2000;Loi et al, 2001;Trounce and Pikert, 2007) between the phylogenetically distant Bubalus and Bos genera (MacEachern et al, 2009). Moreover, detailed screening for buffalo mtDNA in offspring using a real-time protocol able to detect as little as 0.01% of buffalo mtDNA, was unsuccessful in identifying any vestige of buffalo mtDNA in somatic (blood, skin, muscle, and liver) and germline (oocytes) tissues of both calves born from XOT.…”

Section: Resultsmentioning

confidence: 99%

Xenooplasmic Transfer between Buffalo and Bovine Enables Development of Homoplasmic Offspring

Chiaratti¹,

Ferreira

Meirelles³

et al. 2010

Cellular Reprogramming

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Nuclear-mitochondrial incompatibilities may be responsible for the development failure reported in embryos and fetuses produced by interspecies somatic cell nuclear transfer (iSCNT). Herein we performed xenooplasmic transfer (XOT) by introducing 10 to 15% of buffalo ooplasm into bovine zygotes to assess its effect on the persistence of buffalo mitochondrial DNA (mtDNA). Blastocyst rates were not compromised by XOT in comparison to both in vitro fertilized embryos and embryos produced by transfer of bovine ooplasm into bovine zygotes. Moreover, offspring were born after transfer of XOT embryos to recipient cows. Buffalo mtDNA introduced in zygotes was still present at the blastocyst stage (8.3 vs. 9.3%, p ¼ 0.11), indicating unaltered heteroplasmy during early development. Nonetheless, no vestige of buffalo mtDNA was found in offspring, indicating a drift to homoplasmy during later stages of development. In conclusion, we show that the buffalo mtDNA introduced by XOT into a bovine zygote do not compromise embryo development. On the other hand, buffalo mtDNA was not inherited by offspring indicating a possible failure in the process of interspecies mtDNA replication.

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“…1). Hemiplasy ) is consid-ered likely when the internodes are short and the polymorphism persists for relatively short time periods (~3 my; Stefansson et al 2005, Robinson and Ropiquet 2011and MacEachern et al 2009 suggest 5-8 my for the lineage sorting of polymorphic sites in autosomal genes). Under hemiplasy, both the 1p/1q prox + 1q dist and 2prox + 2dist syntenies were present as polymorphic rearrangements at node A and the alternative forms were fixed idiosyncratically in different species.…”

Section: Mode and Tempo Of Chromosomal Evolution Within Rattinimentioning

confidence: 99%

Chromosomal evolution in Rattini (Muridae, Rodentia)

et al. 2011

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The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoofluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BACmapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequencebased phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.

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Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae)

Cited by 62 publications

References 48 publications

Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

Xenooplasmic Transfer between Buffalo and Bovine Enables Development of Homoplasmic Offspring

Chromosomal evolution in Rattini (Muridae, Rodentia)

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