Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Njuguna, Wambui; Liston, Aaron; Cronn, Richard; Ashman, Tia‐Lynn; Bassil, Nahla V.

doi:10.1016/j.ympev.2012.08.026

Cited by 141 publications

(212 citation statements)

References 65 publications

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“…We chose four fossil constraints that were also used in the most recent and comprehensive angiosperm-wide temporal analyses and were in accordance with Magallón et al (2015). Following Njuguna et al (2013), the minimum age for the Prunus/Malus split was set to 48.4 mya (Benedict et al, 2011) and the Castanea/Cucumis split to 84 mya (Sims et al, 1999;Moore et al, 2010). Following Bell et al (2010), the minimum age for Mangifera/Citrus was set to 65 mya (Knobloch and Mai, 1986) and for Oenothera/Eucalyptus to 88.2 mya (Takahashi et al, 1999).…”

Section: Divergence Time Estimation and Fossil Calibrationmentioning

confidence: 99%

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

et al. 2015

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The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ;20 million years ago, coinciding with the Oligocene-toMiocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.

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Section: Divergence Time Estimation and Fossil Calibrationmentioning

confidence: 99%

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

et al. 2015

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“…It is morphologically intermediate to the parental species (Salamone et al, in preparation;Staudt, 1999) and currently exists in a narrow hybrid zone that stretches from southern British Columbia to northern California (Staudt, 1999). Although the two progenitor species last shared a common ancestor 400 000-1 770 000 years ago based on the 95% highest posterior density of a Bayesian dating analysis (Njuguna et al, 2012), the timing of secondary contact is unknown. Staudt (1989) speculated that hybridization occurred after glaciation in the Fraser River valley of British Columbia receded.…”

Section: Species Description and Study Populationsmentioning

confidence: 99%

“…cuneifolia individuals, we screened each individual for two single-nucleotide polymorphisms that differentiate F. virginiana and F. chiloensis chloroplast genomes (Njuguna et al, 2012;Salamone et al, in preparation). Single-nucleotide polymorphisms Sex chromosome variation in hybrid Fragaria R Govindarajulu et al within the intron of petD and an exon of ndhF were screened in 32 plants per population using the dCAPs technique (Neff et al, 1998).…”

Section: Cytotypingmentioning

confidence: 99%

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

2012

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We studied the natural hybrid (Fragaria Â ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or both maternal species, (2) the sex-determining chromosome of the hybrid reflects the location of male sterility within the maternal donor species and (3) crosses from the hybrid species show less sexual dimorphism than the parental species. We found that F. Â ananassa subsp. cuneifolia populations consisted of both parental cytotypes but one predominated within each population. Genetic linkage mapping of two crosses showed dominance of male sterility similar to the parental species, however, the map location of male sterility reflected the maternal donor in one cross, but not the other. Moreover, female function mapped to a single region in the first cross, but to two regions in the second cross. Aside from components of female function (fruit set and seed set), other traits that have been found to be significantly sexually dimorphic in the pure species were either not dimorphic or were dimorphic in the opposite direction to the parental species. These results suggest that hybrids experience some disruption of dimorphism in secondary sexual traits, as well as novel location and number of quantitative trait locus (QTL) affecting sex function.

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“…A previous study reported that incongruence can be caused by a very small number of characters that are in conflict with other sources of data and excluding part of the data would be warranted only if we knew a priori which part of our data is unreliable [40]. Potential incongruence between chloroplast DNA and mitochondrial DNA markers has been reported [92,93]. .…”

Section: Discussionmentioning

confidence: 90%

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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Abstract:In this study, the organelle genomes of Polytrichum juniperinum Hedw. and Polytrichum strictum Menzies ex Brid. (Polytrichaceae, Bryophyta) from Antarctica were sequenced and compared with the plastomes of the model moss species Physcomitrella patens Brid. The sizes of the cpDNA in P. juniperinum and P. strictum were estimated to be 55,168 and 20,183 bp, respectively; the sizes of the mtDNA were 88,021 and 58,896 bp, respectively. The genomes are very similar to each other, with the possible loss of petN in the cpDNA, which also showed some gene inversions when compared with the cpDNAs of P. patens Brid. In the mtDNA, it is possible that rps10 was lost. In contrast, Antarctic Polytrichaceae species have nad7 and orf187, without the occurrence of rearrangement events. Phylogenomic analyses of the plastid and mitochondria revealed that the majority-rule tree suggests some differences in the plastids ancestry, however, P. juniperinum and P. strictum were grouped in the same clade in chloroplast, but in mitochondria P. strictum was grouped with Atrichum angustatum (Brid.) Bruch & Schimp. This study helped us understand the evolution of plastomes and chondriosomes in the family Polytrichaceae, and suggest a hybridization event with relation to the mitochondrial data.

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Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Cited by 141 publications

References 65 publications

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

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