Comparative Analysis of Complete Chloroplast Genome Sequences and Insertion-Deletion (Indel) Polymorphisms to Distinguish Five Vaccinium Species

Kim, Yonguk; Shin, Jawon; Oh, Dool-Ri; Kim, Ah-Young; Choi, Chulyung

doi:10.3390/f11090927

Cited by 17 publications

(29 citation statements)

References 29 publications

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“…This difference between assemblies is reflected in the lower sequence identity shown within the IRs. Greater sequence divergence within the IRs was also reported in a previous comparison between five other Vaccinium species [39]. Indeed, expansion/contraction of the IRs is one of the major causes for plastome size differences between plant species [32].…”

Section: Discussionsupporting

confidence: 56%

“…Vaccinium species [39]. Indeed, expansion/contraction of the IRs is one of the major causes for plastome size differences between plant species [32].…”

Section: Discussionmentioning

confidence: 99%

“…The six Vaccinium cpDNA assemblies were screened for the presence of simple sequence repeats (SSRs), identifying between 77 (lowbush) and 109 (rabbiteye) SSRs (Table S5, Table S6). Mononucleotide repeats were most frequent repeat type found (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41), followed by tetra- (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28) and dinucleotide repeats . Trinucleotide repeats were found in lesser numbers (6)(7)(8) and pentanucleotide repeats were identified only in bilberry (4) and cranberry (6).…”

Section: Simple Sequence Repeat Analysismentioning

confidence: 99%

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Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

Fahrenkrog

Matsumoto

Tóth

et al. 2022

Preprint

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Vaccinium is an economically important genus of berry crops in the family Ericaceae. Given the numerous hybridizations and polyploidization events among Vaccinium species, the taxonomy of this genus has remained uncertain and the subject of long debate. Therefore, the availability of more genomic resources for Vaccinium can provide useful tools for phylogenetic resolution, species identification, authentication of berry food products, and a framework for genetic engineering. In this study, we assembled five Vaccinium chloroplast sequences representing the following berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Two complete plastid genomes were achieved using long-read PacBio sequencing, while three draft sequences were obtained using short-read Illumina sequencing. Comparative analyses also included other previously available Vaccinium chloroplast sequences, especially the commercially important species V. macrocarpon (cranberry). The Vaccinium chloroplast genomes exhibited a circular quadripartite structure, with an overall highly conserved synteny and sequence identity among them. Despite their high similarity, we identified some polymorphic regions in terms of expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, and single nucleotide polymorphisms. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events during northern and southern highbush blueberry domestication. Additional whole plastome analyses including more samples and wild species will be useful to obtain a refined knowledge of the maternal breeding history of blueberries and increase phylogenetic resolution at low taxonomic levels.

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Section: Discussionsupporting

confidence: 56%

“…Vaccinium species [39]. Indeed, expansion/contraction of the IRs is one of the major causes for plastome size differences between plant species [32].…”

Section: Discussionmentioning

confidence: 99%

Section: Simple Sequence Repeat Analysismentioning

confidence: 99%

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Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

Fahrenkrog

Matsumoto

Tóth

et al. 2022

Preprint

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“…The base composition of the assembly is A = 31.61%, C = 18.69%, G = 18.03%, T = 31.65%, and it consists of 32 transfer RNA genes, 5 ribosomal RNA genes, and 115 protein coding genes. The chloroplast of big berry manzanita is smaller than that of R. pulchrum (136 249 bp; Shen et al 2019 ), R. simsii (152 214 bp; Yang et al 2020 ), V. macrocarpon , and four additional Vaccinium species (173 245 bp ~176 045 bp; Kim et al 2020 ). Not surprisingly, the big berry manzanita chloroplast assembly is an order of magnitude larger than the highly reduced chloroplast genome of the saprophytic and non-photosynthesizing H. monotropa (35 336 bp; Gruzdev et al 2016 ).…”

Section: Resultsmentioning

confidence: 93%

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Huang

Escalona

Morrison

et al. 2021

Journal of Heredity

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Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.

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“…Increasingly, transcriptomics experiments for Vaccinium have been reported in recent years, including lingonberry (Tian et al, 2020), cranberry (Sun et al, 2015), blueberry (Günther et al, 2020; Li et al, 2016; Zhang et al, 2020) and bilberry (Nguyen et al, 2018). Recently the chloroplast genomes of five Vaccinium species ( V. bracteatum , V. vitis ‐ idaea , V. uliginosum , V. macrocarpon , and V. oldhamii ) have been described, with a view both to improve the phylogenetics and assist with authentication of species with greater accuracy (Kim et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

Deng

Hilario

et al. 2021

Molecular Ecology Resources

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Bilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi‐C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker‐trait association between these two species, as the loci involved in key characters are orthologous.

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Comparative Analysis of Complete Chloroplast Genome Sequences and Insertion-Deletion (Indel) Polymorphisms to Distinguish Five Vaccinium Species

Cited by 17 publications

References 29 publications

Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

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