Plant phylogeography based on organelle genes: an introduction

2007 ◽  
pp. 23-97 ◽  
Author(s):  
Rémy J. Petit ◽  
Giovanni G. Vendramin
Keyword(s):  
Organelle Genes

Comparison of Allozyme and Mitochondrial DNA Variation in Populations of Walleye, Stizostedion vitreum

1989 ◽  
Vol 46 (12) ◽  
pp. 2074-2084 ◽  
Author(s):  
Robert D. Ward ◽  
Neil Billington ◽  
Paul D. N. Hebert
Keyword(s):  
Mitochondrial Dna ◽  
Glacial Refugia ◽  
Divergence Times ◽  
Stizostedion Vitreum ◽  
Dna Variation ◽  
Mtdna Variation ◽  
Mtdna Haplotypes ◽  
Total Genetic Diversity ◽  
Allozyme Loci ◽  
Organelle Genes

Twelve populations of walleye (Stizostedion vitreum) from the Great Lakes and three populations from northern Manitoba were screened for allozyme and mitochondrial DNA (mtDNA) variation. Nine enzyme loci known to show genetic variation were screened in all fish: five of them (Prot-4, Prot-2, Mdh-3, Idh-1, Adh) showed appreciable polymorphism. MtDNA was examined in all fish using six endonucleases that detected polymorphic sites and a further 13 endonucleases that detected only monomorphic sites. Only one of the allozyme loci (Prot-4) showed evidence of geographic patterning of allele frequencies. By contrast, the mtDNA haplotypes showed clear geographic variation. The proportion of total genetic diversity attributable to population differentiation (Gst) was three to five times greater for mtDNA than for the allozymes. Gst values for organelle genes are expected on theoretical grounds to be greater than for nuclear genes, and this expected difference may be enhanced in walleye because of the likelihood that, in this species, male-mediated gene flow exceeds that of females. The distributions of mtDNA haplotypes and estimated divergence times are consistent with the derivation of extant walleye populations from three different glacial refugia.

scholarly journals Uniparental inheritance of organelle genes

2008 ◽  
Vol 18 (16) ◽  
pp. R692-R695 ◽  
Author(s):  
C. William Birky
Keyword(s):  
Uniparental Inheritance ◽  
Organelle Genes

Organelle genes – do they jump or are they pushed?

2000 ◽  
Vol 16 (2) ◽  
pp. 65-66 ◽  
Author(s):  
Christopher J. Howe ◽  
Adrian C. Barbrook ◽  
Peter J. Lockhart
Keyword(s):  
Organelle Genes

scholarly journals Nonneutral Evolution of Organelle Genes inSilene vulgaris

Genetics ◽  
2006 ◽  
Vol 174 (4) ◽  
pp. 1983-1994 ◽  
Author(s):  
Gary J. Houliston ◽  
Matthew S. Olson
Keyword(s):  
Organelle Genes

scholarly journals Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera

2020 ◽  
Vol 12 (3) ◽  
pp. 203-209
Author(s):  
Eiichi Shoguchi ◽  
Yuki Yoshioka ◽  
Chuya Shinzato ◽  
Asuka Arimoto ◽  
Debashish Bhattacharya ◽  
...  
Keyword(s):  
Rna Editing ◽  
Phylogenetic Analyses ◽  
Snp Analysis ◽  
Ryukyu Archipelago ◽  
The North ◽  
Acropora Digitifera ◽  
Organelle Genomes ◽  
Molecular Phylogenetic ◽  
Symbiotic Dinoflagellates ◽  
Organelle Genes

Abstract In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.

scholarly journals Comparative and phylogenomic analysis of nuclear and organelle genes in cryptic Coelastrella vacuolata MACC-549 green algae

2021 ◽  
Vol 58 ◽  
pp. 102380
Author(s):  
Prateek Shetty ◽  
Attila Farkas ◽  
Bernadett Pap ◽  
Bettina Hupp ◽  
Vince Ördög ◽  
...  
Keyword(s):  
Green Algae ◽  
Phylogenomic Analysis ◽  
Organelle Genes

The inheritance of organelle genes and genomes: patterns and mechanisms

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 951-958 ◽  
Author(s):  
Jianping Xu
Keyword(s):  
Recent Observation ◽  
Research Progress ◽  
Interspecific Crosses ◽  
Uniparental Inheritance ◽  
Organelle Inheritance ◽  
Inheritance Patterns ◽  
Paternal Leakage ◽  
Eukaryotic Microorganisms ◽  
Multicellular Organisms ◽  
Organelle Genes

Unlike nuclear genes and genomes, the inheritance of organelle genes and genomes does not follow Mendel's laws. In this mini-review, I summarize recent research progress on the patterns and mechanisms of the inheritance of organelle genes and genomes. While most sexual eukaryotes show uniparental inheritance of organelle genes and genomes in some progeny at least part of the time, increasing evidence indicates that strictly uniparental inheritance is rare and that organelle inheritance patterns are very diverse and complex. In contrast with the predominance of uniparental inheritance in multicellular organisms, organelle genes in eukaryotic microorganisms, such as protists, algae, and fungi, typically show a greater diversity of inheritance patterns, with sex-determining loci playing significant roles. The diverse patterns of inheritance are matched by the rich variety of potential mechanisms. Indeed, many factors, both deterministic and stochastic, can influence observed patterns of organelle inheritance. Interestingly, in multicellular organisms, progeny from interspecific crosses seem to exhibit more frequent paternal leakage and biparental organelle genome inheritance than those from intraspecific crosses. The recent observation of a sex-determining gene in the basidiomycete yeast Cryptococcus neoformans, which controls mitochondrial DNA inheritance, has opened up potentially exciting research opportunities for identifying specific molecular genetic pathways that control organelle inheritance, as well as for testing evolutionary hypotheses regarding the prevalence of uniparental inheritance of organelle genes and genomes.Key words: isogamy, anisogamy, paternal leakage, mating type, quantitative organelle inheritance.

Phylogenetic transfer of organelle genes to the nucleus can lead to new mechanisms of protein integration into membranes

1999 ◽  
Vol 17 (1) ◽  
pp. 31-40 ◽  
Author(s):  
Doris Michl ◽  
Ivan Karnauchov ◽  
Jürgen Berghöfer ◽  
Reinhold G. Herrmann ◽  
Ralf Bernd Klösgen
Keyword(s):  
Organelle Genes

scholarly journals Mating system and the critical migration rate for swamping selection

2011 ◽  
Vol 93 (3) ◽  
pp. 233-254 ◽  
Author(s):  
XIN-SHENG HU
Keyword(s):  
Mating System ◽  
Migration Rate ◽  
Nuclear Gene ◽  
Directional Selection ◽  
Pollen Flow ◽  
Mixed Mating ◽  
Mixed Mating System ◽  
Selection Scheme ◽  
Complementary Relationship ◽  
Organelle Genes

SummaryCrow et al. (1990) and Barton (1992) have examined the critical migration rate for swamping selection in the nuclear system. Here, I use the same methodology to examine the critical migration rate in the cytonuclear system for hermaphrodite plants with a mixed mating system. Two selection schemes for a nuclear gene (heterozygote disadvantage and directional selection) and the directional selection scheme for organelle genes are considered. Results show that under random mating, the previous results are applicable to plant species by appropriate re-parameterization of the migration rate for nuclear and paternal organelle genes. A simple complementary relationship exists between seed and pollen flow in contributing to the critical migration rate. Under the mixed mating system, the critical migration rate of seeds and pollen for nuclear and paternal organelle genes can be changed due to the effects of selection and the cytonuclear linkage disequilibrium generated by migration and inbreeding. A negative but not complementary relationship exists between seed and pollen flow in contributing to the critical migration rate, varying with the mating system. Partial selfing can also adjust the critical seed flow for the maternal organelle gene, with a small critical migration rate for species of a high selfing rate. Both concordance and discordance among cytonuclear genes can occur under certain conditions during the process of swamping selection. This theory predicts the presence of various contributions of seed versus pollen flow to genetic swamping for plants with diverse mating systems.

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