Recco: recombination analysis using cost optimization

Maydt, Jochen; Lengauer, Thomas

doi:10.1093/bioinformatics/btl057

Cited by 104 publications

(95 citation statements)

References 30 publications

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“…In the present study, we determined the haplotype of sequences, excluding the outgroup, using the DnaSP 5.0 program (Librado and Rozas, 2009) and constructed a network of the Elymus species using the Network 4.1 program (Fluxus Technology Ltd, Clare, Suffolk, UK). Recombination was tested using the Recco program (Maydt and Lengauer, 2006) and the MJ network was analyzed using non-recombining sequences.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis of Elymus (Poaceae) in western China

2015

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ABSTRACT. Elymus L. is often planted in temperate and subtropical regions as forage. Species in the genus have 5 allopolyploid genomes that are found in the grass tribe Triticeae. To determine the phylogenetic relationships in Elymus species from western China, we estimated phylogenetic trees using sequences from the nuclear ribosomal internal transcribed spacer and non-coding chloroplast DNA sequences from 56 accessions (871 samples) of 9 polyploid Elymus species and 42 accessions from GenBank. Tetraploid and hexaploid Elymus species from western China had independent origins, and Elymus species from the same area or neighboring geographic regions were the most closely related. Based on the phylogenetic tree topology, the St-and Y-genomes were not derived from the same donor and Y-genome likely originated from the H-genome of Hordeum species, or they shared the same origin or underwent introgression. The maternal genome of tetraploid and hexaploid Elymus species originated from species of Hordeum or Pseudoroegneria.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis of Elymus (Poaceae) in western China

2015

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“…Full-length SIVgor sequences were analyzed using bootscan and similarity plots with SimPlot version 3.5.1 and Recco version 0.93 (59,60). Bootscan analyses examined neighbor-joining trees with a 400-bp window and 20-bp increments.…”

Section: Methodsmentioning

confidence: 99%

Origin of the HIV-1 group O epidemic in western lowland gorillas

D’arc

Ayouba

Esteban

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

136

149

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HIV-1, the cause of AIDS, is composed of four phylogenetic lineages, groups M, N, O, and P, each of which resulted from an independent cross-species transmission event of simian immunodeficiency viruses (SIVs) infecting African apes. Although groups M and N have been traced to geographically distinct chimpanzee communities in southern Cameroon, the reservoirs of groups O and P remain unknown. Here, we screened fecal samples from western lowland (n = 2,611), eastern lowland (n = 103), and mountain (n = 218) gorillas for gorilla SIV (SIVgor) antibodies and nucleic acids. Despite testing wild troops throughout southern Cameroon (n = 14), northern Gabon (n = 16), the Democratic Republic of Congo (n = 2), and Uganda (n = 1), SIVgor was identified at only four sites in southern Cameroon, with prevalences ranging from 0.8–22%. Amplification of partial and full-length SIVgor sequences revealed extensive genetic diversity, but all SIVgor strains were derived from a single lineage within the chimpanzee SIV (SIVcpz) radiation. Two fully sequenced gorilla viruses from southwestern Cameroon were very closely related to, and likely represent the source population of, HIV-1 group P. Most of the genome of a third SIVgor strain, from central Cameroon, was very closely related to HIV-1 group O, again pointing to gorillas as the immediate source. Functional analyses identified the cytidine deaminase APOBEC3G as a barrier for chimpanzee-to-gorilla, but not gorilla-to-human, virus transmission. These data indicate that HIV-1 group O, which spreads epidemically in west central Africa and is estimated to have infected around 100,000 people, originated by cross-species transmission from western lowland gorillas.

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“…Genetic diversity was measured, both within the Gambian SIVagmSab cluster and between other SIVagm clusters from the reference alignment, using MEGA v5.10 (65). Recombination was screened for by using Recco (66), SBP/GARD (67), and SplitsTree (68). Maximum likelihood molecular phylogenetic trees were computed separately for gag, pol, and env alignments, using RAxML v7.4.6 (69) using the general time reversible (GTR) substitution model and gamma distributed rate heterogeneity.…”

Section: Figmentioning

confidence: 99%

Factors Associated with Siman Immunodeficiency Virus Transmission in a Natural African Nonhuman Primate Host in the Wild

Jasinska

Feyertag

et al. 2014

J Virol

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African green monkeys (AGMs) are naturally infected with simian immunodeficiency virus (SIV) at high prevalence levels and do not progress to AIDS. Sexual transmission is the main transmission route in AGM, while mother-to-infant transmission (MTIT) is negligible. We investigated SIV transmission in wild AGMs to assess whether or not high SIV prevalence is due to differences in mucosal permissivity to SIV (i.e., whether the genetic bottleneck of viral transmission reported in humans and macaques is also observed in AGMs in the wild). We tested 121 sabaeus AGMs (Chlorocebus sabaeus) from the Gambia and found that 53 were SIV infected (44%). By combining serology and viral load quantitation, we identified 4 acutely infected AGMs, in which we assessed the diversity of the quasispecies by single-genome amplification (SGA) and documented that a single virus variant established the infections. We thus show that natural SIV transmission in the wild is associated with a genetic bottleneck similar to that described for mucosal human immunodeficiency virus (HIV) transmission in humans. Flow cytometry assessment of the immune cell populations did not identify major differences between infected and uninfected AGM. The expression of the SIV coreceptor CCR5 on CD4 ؉ T cells dramatically increased in adults, being higher in infected than in uninfected infant and juvenile AGMs. Thus, the limited SIV MTIT in natural hosts appears to be due to low target cell availability in newborns and infants, which supports HIV MTIT prevention strategies aimed at limiting the target cells at mucosal sites. Combined, (i) the extremely high prevalence in sexually active AGMs, (ii) the very efficient SIV transmission in the wild, and (iii) the existence of a fraction of multiparous females that remain uninfected in spite of massive exposure to SIV identify wild AGMs as an acceptable model of exposed, uninfected individuals. IMPORTANCEWe report an extensive analysis of the natural history of SIVagm infection in its sabaeus monkey host, the African green monkey species endemic to West Africa. Virtually no study has investigated the natural history of SIV infection in the wild. The novelty of our approach is that we report for the first time that SIV infection has no discernible impact on the major immune cell populations in natural hosts, thus confirming the nonpathogenic nature of SIV infection in the wild. We also focused on the correlates of SIV transmission, and we report, also for the first time, that SIV transmission in the wild is characterized by a major genetic bottleneck, similar to that described for HIV-1 transmission in humans. Finally, we report here that the restriction of target cell availability is a major correlate of the lack of SIV transmission to the offspring in natural hosts of SIVs.

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Recco: recombination analysis using cost optimization

Cited by 104 publications

References 30 publications

Phylogenetic analysis of Elymus (Poaceae) in western China

Phylogenetic analysis of Elymus (Poaceae) in western China

Origin of the HIV-1 group O epidemic in western lowland gorillas

Factors Associated with Siman Immunodeficiency Virus Transmission in a Natural African Nonhuman Primate Host in the Wild

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