Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line

Nikiforova, Svetlana V.; Cavalieri, Duccio; Velasco, Riccardo; Goremykin, Vadim V.

doi:10.1093/molbev/mst092

Cited by 102 publications

(92 citation statements)

References 43 publications

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“…The results from Coart et al (2006) are in line with those recently reported based on the analysis of a dataset including 46 completely or nearly completely sequenced chloroplast genomes sampled across the genus Malus (Nikiforova et al 2013): the latter study indicated that M. sylvestris contributed the chloroplast genome to the majority of M. × domestica cultivars they examined. Note, however, that the domesticated apple probably did not arise from a single event over a short period of time, but from evolution extending over thousands of years.…”

Section: Chloroplast Dna Polymorphismsupporting

confidence: 82%

Cytoplasmic genome diversity in the cultivated apple - Short Communication

Mikami

Kitazaki

Kishima

2015

Hort. Sci. (Prague)

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Mikami T., Kitazaki K., Kishima Y. (2015): Cytoplasmic genome diversity in the cultivated apple -Short Communication. Hort. Sci. (Prague), 42: 47-51.The cultivated apple is one of the most common and important fruit crops in temperate regions. Phylogenetic analysis using a wide array of apple genotypes could give insights into the origin and domestication history of this crop. Maternally inherited mitochondrial and chloroplast DNAs have been utilised to characterise the cytoplasmic diversity within the apple germplasm collection and to elucidate the relationships between the cytoplasm types defined. This review focuses on the molecular basis of changes in the mitochondrial genome giving rise to diverse cytoplasm types. The possible maternal lineage of the cultivated apple is also discussed.

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Section: Chloroplast Dna Polymorphismsupporting

confidence: 82%

Cytoplasmic genome diversity in the cultivated apple - Short Communication

Mikami

Kitazaki

Kishima

2015

Hort. Sci. (Prague)

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“…There are examples of where whole chloroplast sequences have been used to measure phylogeny and estimate divergence times of closely related species. This was utilized previously [49], where chloroplast genomes from 47 apple taxa were used, including both wild and domesticated taxa. By using the whole chloroplast sequence, a complete phylogeny and estimates of divergence times of the taxa could be obtained [49].…”

Section: Discussionmentioning

confidence: 99%

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

et al. 2014

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Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

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“…sikkimensis and M. spectabilis were not included in the phylogenetic analyses of SbeI gene sequences due to a lack of samples. Nonetheless, M. sieboldii could be used as a representative of the maternal lineage as phylogenetic analysis of Malus chloroplast genomes indicated a relatively close affinity among M. sieboldii , M. sikkimensis , and M. spectabilis (Nikiforova et al, ). The S1‐type SbeI sequences identified in M. sieboldii and M. toringoides belong to a well‐supported clade (clade I in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…§Chloroplast haplotypes of M. transitoria , M. kansuensis , and M. toringoides as well as the three new hybrids were inferred from the chloroplast sequences generated in this study; chloroplast haplotypes of other Malus species were inferred based on the chloroplast sequences retrieved from Nikiforova et al ().…”

Section: Methodsmentioning

confidence: 96%

New insights into the hybrid origin of Malus toringoides and its close relatives based on a single‐copy nuclear gene SbeI and three chloroplast fragments

Tang

Tan

et al. 2014

J of Sytematics Evolution

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Malus toringoides Hughes and its close relatives, M. maerkangensis M. H. Cheng et al., M. setok Vassilcz., and M. xiaojinensis M. H. Cheng & N. G. Jiang were supposed to derive from hybridizations. However, molecular data are still inadequate to corroborate the hybrid origin hypotheses. In this study, we sequenced a single-copy nuclear gene SbeI and three chloroplast fragments and carried out phylogenetic analyses to investigate the evolutionary origins of the above four putative hybrid taxa. The hybrid nature of M. toringoides is confirmed by the detection of two distinct types of SbeI sequences from it. The chloroplast and SbeI gene phylogenies show that the maternal progenitor of M. toringoides is closely related to M. sikkimensis N. P. Balakr. and M. spectabilis Borkh., and the paternal progenitor is most likely M. transitoria C. K. Schneid. The hypothesis that M. kansuensis (Batalin) C. K. Schneid. is one of the parents of M. toringoides is not supported. Malus maerkangensis and M. xiaojinensis might have originated through hybridization between M. toringoides and M. kansuensis, whereas M. setok is genetically closely related to M. toringoides. The three close relatives of M. toringoides were designated as three novel species by some researchers, however, as they were all apomictic with limited distribution areas and they originated from hybridization and polyploidization, we recommend that their species status should be re-evaluated.

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Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line

Cited by 102 publications

References 43 publications

Cytoplasmic genome diversity in the cultivated apple - Short Communication

Cytoplasmic genome diversity in the cultivated apple - Short Communication

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

New insights into the hybrid origin of Malus toringoides and its close relatives based on a single‐copy nuclear gene SbeI and three chloroplast fragments

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