Pacbio Sequencing Reveals Identical Organelle Genomes between American Cranberry (Vaccinium macrocarpon Ait.) and a Wild Relative

Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry, and could be useful to improve fruit quality such as phytochemical content. Furthermore, given their northern distribution, they could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, the Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos.

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Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

10.1101/567925 ◽

2019 ◽

Author(s):

Luis Diaz-Garcia ◽

Lorraine Rodriguez-Bonilla ◽

Tyler Smith ◽

Juan Zalapa

Keyword(s):

Phenotypic Diversity ◽

Phenotypic Variability ◽

Wild Relative ◽

Nucleotide Polymorphisms ◽

Pacbio Sequencing ◽

High Coverage ◽

Phytochemical Content ◽

Plastid Genomes ◽

Organelle Genomes ◽

American Cranberry

AbstractBreeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials.Vaccinium microcarpum(Turcz. ex Rupr.) Schmalh. andV. oxycoccosL., two closely related species, may be cross-compatible with the American cranberry and could be useful to improve fruit quality such as phytochemical content, and given their northern distribution, could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative,V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, Illumina resequencing of additional accessions ofV. microcarpumandV. oxycoccosrevealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal ofV. microcarpum. Finally, we provided important data regarding the polyploid origin ofV. oxycoccos.

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Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

Frontiers in Plant Science ◽

10.3389/fpls.2021.633310 ◽

2021 ◽

Vol 12 ◽

Author(s):

Luis Diaz-Garcia ◽

Luis Fernando Garcia-Ortega ◽

Maria González-Rodríguez ◽

Luis Delaye ◽

Massimo Iorizzo ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Assembly ◽

Anthocyanin Biosynthesis ◽

Draft Genome ◽

Vaccinium Macrocarpon ◽

Wild Relative ◽

Fruit Crop ◽

Sexual And Asexual Reproduction ◽

American Cranberry ◽

Chromosome Level

The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.

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Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

PeerJ ◽

10.7717/peerj.9309 ◽

2020 ◽

Vol 8 ◽

pp. e9309

Author(s):

Viktoria Yu Shtratnikova ◽

Mikhail I. Schelkunov ◽

Aleksey A. Penin ◽

Maria D. Logacheva

Keyword(s):

Mitochondrial Genome ◽

Rna Editing ◽

Transcriptome Sequencing ◽

Unique Feature ◽

Genetic Material ◽

Mitochondrial Genes ◽

Vaccinium Macrocarpon ◽

Mitochondrial Genomes ◽

Plastid Genomes ◽

Trans Splicing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

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Alteration of Anthocyanin Glycosylation in Cranberry Through Interspecific Hybridization

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.5.711 ◽

2005 ◽

Vol 130 (5) ◽

pp. 711-715 ◽

Cited By ~ 21

Author(s):

Nicholi Vorsa ◽

James J. Polashock

Keyword(s):

Human Health ◽

Interspecific Hybridization ◽

Interspecific Hybrids ◽

Parental Species ◽

Genetic Manipulation ◽

Vaccinium Macrocarpon ◽

Antioxidant Potential ◽

Backcross Population ◽

American Cranberry

The flavonoids of american cranberry (Vaccinium macrocarpon Ait.) are documented to be beneficial for human health. Among their benefits is a high antioxidant potential, with anthocyanin glycosides being the main contributors. Flavonoid glucose conjugates are reported to be more bioavailable than those with other sugar conjugates. The anthocyanin glycosides of V. macrocarpon fruit are mainly galactosides and arabinosides of the aglycones, cyanidin and peonidin, with less than 8% glucosides. In contrast, the fruit anthocyanins of another cranberry species, V. oxycoccus L. were found to be largely glucosides of cyanidin and peonidin. Interspecific hybrids between these two species were intermediate to the parental species in the proportion of fruit anthocyanin glucosides. About half the progeny (1:1 segregation) in a backcross population (to V. macrocarpon) maintained the relatively high anthocyanin glucoside ratio. In this study, we demonstrate the genetic manipulation of anthocyanin glycosylation in cranberry using interspecific hybridization, resulting in dramatically increased glucose-conjugated anthocyanins.

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Seed lipids of the American cranberry (vaccinium macrocarpon)

Phytochemistry ◽

10.1016/s0031-9422(00)88185-6 ◽

1969 ◽

Vol 8 (11) ◽

pp. 2219-2222 ◽

Cited By ~ 9

Author(s):

Rodney Croteau ◽

Irving S. Fagerson

Keyword(s):

Vaccinium Macrocarpon ◽

Seed Lipids ◽

American Cranberry

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Antibacterial activities of a polyphenolic-rich extract prepared from American cranberry (Vaccinium macrocarpon) fruit pomace against Listeria spp.

LWT ◽

10.1016/j.lwt.2020.109056 ◽

2020 ◽

Vol 123 ◽

pp. 109056 ◽

Cited By ~ 4

Author(s):

Moussa S. Diarra ◽

Yousef I. Hassan ◽

Glenn S. Block ◽

John C.G. Drover ◽

Pascal Delaquis ◽

...

Keyword(s):

Antibacterial Activities ◽

Vaccinium Macrocarpon ◽

American Cranberry ◽

Fruit Pomace

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Variability in the Qualitative and Quantitative Composition and Content of Phenolic Compounds in the Fruit of Introduced American Cranberry (Vaccinium macrocarpon Aiton)

Plants ◽

10.3390/plants9101379 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1379

Author(s):

Ieva Gudžinskaitė ◽

Elicija Stackevičienė ◽

Mindaugas Liaudanskas ◽

Kristina Zymonė ◽

Vaidotas Žvikas ◽

...

Keyword(s):

Phenolic Compounds ◽

Vaccinium Macrocarpon ◽

Quantitative Composition ◽

Qualitative And Quantitative ◽

American Cranberry ◽

Fruit Samples ◽

Phytochemical Profile ◽

Ethanol Extracts ◽

The Individual

The aim of this study was to determine the composition and content of phenolic compounds in ethanol extracts of eight different cultivars of American cranberry (Vaccinium macrocarpon Aiton) fruit using spectrophotometric and UPLC-ESI-MS/MS analysis and to evaluate the antioxidant activity in vitro of these extracts. The highest total amount of phenolic compounds evaluated via Folin–Ciocalteu spectrophotometry was detected in American cranberry fruit samples of the ‘Bain’ clone, and the highest total amount of flavonoids was found in samples of the ‘Drever’ and ‘Baiwfay’ cultivars. The highest total amount of the individual phenolic compounds (519.53 ± 25.12 mg/g DW) identified and quantitatively evaluated via chromatography was detected in samples of the ‘Searles’ cranberry cultivar. In the studied cranberry samples, the predominant phenolic compounds were hyperoside, quercetin, and procyanidin A2, while the amounts of other compounds were significantly lower. HCA and PCA revealed that ‘Woolman’, ‘Holliston’, ‘Pilgrim, and ‘Searles’ fruit samples had different quantitative content of phenolic compounds from other cranberry cultivars. Meanwhile, fruit of ‘Baiwfay’, ‘Drever’, ‘Bain’, and ‘Bergman’ were similar in their phytochemical profile.

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