Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

Fajardo, Diego; Senalik, Douglas; Ames, Mercedes; Zhu, Huayu; Steffan, Shawn A.; Harbut, Rebecca; Polashock, James J.; Vorsa, Nicholi; Gillespie, Emily L.; Kron, Kathy; Zalapa, Juan

doi:10.1007/s11295-012-0573-9

Cited by 95 publications

(119 citation statements)

References 33 publications

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“…Comparing with other angiosperm chloroplast genomes, more repeats and tRNA genes occurred near rearrangement endpoints in this species. The positive connection between rearrangement and repeated sequences has also been found in other plants, like Arbutus unedo (Martínez-Alberola et al, 2013), Geraniaceae (Weng et al, 2013), Vaccinium macrocarpon (Fajardo et al, 2013) and cupressophytes (Wu & Chaw, 2014). However, the effects of these chloroplast gene rearrangements on plant physical functions still need more study.…”

Section: Discussionmentioning

confidence: 64%

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

Yao

Liu

Tan

et al. 2016

PeerJ

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Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

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Section: Discussionmentioning

confidence: 64%

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

Yao

Liu

Tan

et al. 2016

PeerJ

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“…The complete chloroplast genome of cranberry has been published [37]. A maximum likelihood (RAxML) tree was built and the results of 100 bootstrap replicates were used to determine branch support in an unrooted phylogeny (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

et al. 2014

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BackgroundThe American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.ResultsThe genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).ConclusionsShotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.

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“…A similar truncation was seen in Quercus aliena (Lu et al, 2016, ycf15 ) and Quercus spinosa (Du et al, 2015) of Fagaceae, in Liliales (Liu et al, 2012b), Kiwi fruit ( Actinidia chinensis var. chinensis) (Yao and Huang, 2016), and Vaccinium macrocarpon (Fajardo et al, 2013). ycf15 is a pseudogene in all families of Saxifragales (Dong et al, 2013), but may be a functional protein coding gene in Thalictrum coreanum (Ranunculaceae, Park et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

2017

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Juglans L. (walnuts and butternuts) is an economically and ecologically important genus in the family Juglandaceae. All Juglans are important nut and timber trees. Juglans regia (Common walnut), J. sigillata (Iron walnut), J. cathayensis (Chinese walnut), J. hopeiensis (Ma walnut), and J. mandshurica (Manchurian walnut) are native to or naturalized in China. A strongly supported phylogeny of these five species is not available due to a lack of informative molecular markers. We compared complete chloroplast genomes and determined the phylogenetic relationships among the five Chinese Juglans using IIumina sequencing. The plastid genomes ranged from 159,714 to 160,367 bp encoding 128 functional genes, including 88 protein-coding genes and 40 tRNA genes each. A complete map of the variability across the genomes of the five Juglans species was produced that included single nucleotide variants, indels (insertions and deletions), and large structural variants, as well as differences in simple sequence repeats (SSR) and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into two previously recognized sections (Juglans/Dioscaryon and Cardiocaryon) with a 100% bootstrap (BS) value using the complete cp genomes, protein coding sequences (CDS), and the introns and spacers (IGS) data. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in Juglans, and also provide insight into utilization of Juglans plants.

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Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

Cited by 95 publications

References 33 publications

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

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