Comparative transcriptome analysis of lingonberry (<i>Vaccinium vitis-idaea</i>) provides insights into genes associated with flavonoids metabolism during fruit development

Tian, Yongqiang; Ma, Zhili; Ma, Haohao; Gu, Yu; Li, Yadong; Sun, Haiyue

doi:10.1080/13102818.2020.1803130

Cited by 9 publications

(17 citation statements)

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“…We annotated more than 73 000 genes for each species, which is comparable with I. walleriana result (70 190). Our results are also comparable with other genera in Ericales order such as Primula (67 201 genes, (66)), Phlox (59 994 genes, (71)), Saltugilia (51 020-92 672 genes,(72)), Camellia (46 223-46 736, (73)) and Vaccinium (35 060 – 67 836 genes (74, 75). GO terms assignment for identified transcripts is surprisingly similar between\ species.…”

Section: Discussionsupporting

confidence: 88%

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Comparative transcriptomics of sevenImpatiensspecies

Šurinová

Stočes²,

Dostálek

et al. 2021

Preprint

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Impatiens is a genus containing more than 1000 species. Thanks to its size, it is a unique system for studying species diversification in natural populations. This study focused on the characterization of novel transcriptomes from seven Impatiens species originating from Nepal. Leave transcriptome of Impatines balsamina L. , I. racemosa DC. , I. bicornuta Wall , I. falcifer Hook , I. devendrae Pusalkar, I. scullyi Hook and I. scabrida DC were sequenced and compared. Reads were de novo assembled and aligned to 92 035-226 081 contigs. We identified 14 728 orthology groups shared among all the species and 3 020 which were unique to a single species. In single species, 2536-3009 orthology groups were under selection from which 767 were common for all species. Six of the seven investigated species shared 77% of gene families with I. bicornuta being the most distinct species. Specific gene families involved in response to different environmental stimuli were closely described. Impatiens bicornuta selection profile shared selection on zing finger protein structures and flowering regulation and stress response proteins with the other investigated species. Overall, the study showed substantial similarity in patterns of selections on transcribed genes across the species suggesting similar evolutionary pressures. This suggests that the species group may have evolved via adaptive radiation.

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Section: Discussionsupporting

confidence: 88%

“…We annotated more than 73 000 genes for each species, which is comparable with I. walleriana result (70 190). Our results are also comparable with other genera in Ericales (74,75). GO terms assignment for identified transcripts is surprisingly similar between species.…”

Section: De Novo Transcriptome Reconstructionsupporting

confidence: 89%

Comparative transcriptomics of sevenImpatiensspecies

Šurinová

Stočes²,

Dostálek

et al. 2021

Preprint

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“…This improved resource provides an assembly resolved to the 48 (4 × 12) homologous chromosomes expected from this species. 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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“…Transcriptome sequencing across berry development allowed for annotation of a total of 64 526 genes across both haplotypes. Although no genome is available for V. vitis-idaea (lingonberry), transcriptome sequence identified 67 836 genes including many differentially expressed during fruit development [ 51 ]. The Genome Database for Vaccinium (GDV, https://www.vaccinium.org ) [ 52 ], the crop community database for Vaccinium , provides access to integrated genomic, genetic, and breeding peer-reviewed published data, and analysis tools.…”

Section: Genomic Transcriptomic and Metabolomic Resources For ...mentioning

confidence: 99%

“…The recent availability of high-quality reference genomes for Vaccinium (blueberry, cranberry, bilberry) and technological advances in RNA-sequencing have also advanced transcriptome profiling. Recent transcriptome studies in Vaccinium have focused on the biosynthesis of metabolites with human health benefits [ 44 , 46 , 51 , 57 – 65 ], cold acclimation [ 66 – 71 ], fruit and flower development [ 72 – 77 ], biotic interactions [ 78 – 82 ], postharvest storage [ 83 , 84 ], roots [ 85 , 86 ], and transcriptome regulatory analysis [ 87 – 89 ]. As of June 2021, there are 543 entries for “ Vaccinium ” in the NCBI Small Read Archive (SRA), encompassing varying species, developmental stages, sequencing technologies, tissue type, and sequencing strategy.…”

Section: Genomic Transcriptomic and Metabolomic Resources For ...mentioning

confidence: 99%

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

Edger

Iorizzo

Bassil

et al. 2022

Horticulture Research

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The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.

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Comparative transcriptome analysis of lingonberry (Vaccinium vitis-idaea) provides insights into genes associated with flavonoids metabolism during fruit development

Abstract: Sun (2020) Comparative transcriptome analysis of lingonberry (Vacciniumvitis-idaea) provides insights into genes associated with flavonoids metabolism during fruit development, Biotechnology &

Cited by 9 publications

References 50 publications

Comparative transcriptomics of sevenImpatiensspecies

Comparative transcriptomics of sevenImpatiensspecies

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

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

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