Phylogeny problems of the genus &lt;i&gt;Vaccinium&lt;/i&gt; L. and ways to solve them

Zhidkin, Roman R.; Matveeva, T. V.

doi:10.17816/ecogen109142

Cited by 4 publications

(2 citation statements)

References 36 publications

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“…Additionally, V. angustifolium seems to have diverged earlier within the Cyanococcus clade. Overall, the rest of the branches agree with the genetic relationships reported between sections in other phylogenetic studies where whole cp genomes have been used [4,80].…”

Section: Discussionsupporting

confidence: 85%

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

et al. 2023

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Vaccinium floribundum, commonly known as mortiño, is a native high Andean wild species of cultural and economic importance. Genomic resources for V. floribundum are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. This study aimed to assemble the complete chloroplast genome sequence of this species and perform an in-depth comparative analysis with other Vaccinium species. The chloroplast genome of V. floribundum was obtained using Oxford Nanopore Technology (ONT). The de novo assembly of the chloroplast genome of V. floribundum resulted in a 187,966 bp sequence, which contained 134 genes (84 Protein Coding Genes (PCGs), 42 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes). The comparative analysis of the V. floribundum chloroplast genome with other nine chloroplast genomes of the Vaccinium species suggested that a contraction/expansion event of the inverted repeat (IR) regions could have occurred, causing the relocation of psbA and rpl32 genes. Additionally, a possible loss of function of the ndhF gene was found. For the phylogenetic analysis based on 87 genes, the chloroplast genome of 19 species (including V. floribundum) was used and revealed that V. myrtillus could be a sister group of V. floribundum. Altogether, our findings provide insights into the plastome characteristics and the phylogeny of V. floribundum. This study describes the complete chloroplast genome sequence of V. floribundum as the first genomic resource available for an Andean species native to Ecuador.

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Section: Discussionsupporting

confidence: 85%

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

et al. 2023

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“…The ITS of hybrid species retain the features of only one parent, and chloroplast markers are inherited mainly through the maternal line [ 40 ]. At the same time, the phylogeny based on genomic data is in better agreement with the traditional system [ 34 , 35 , 41 , 42 ]. Collectively, these data indicate that additional research is required, including the search for new cheap and reliable markers for the molecular phylogeny of Vaccinium .…”

Section: Discussionmentioning

confidence: 81%

Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies

Zhidkin

Zhurbenko

Bogomaz

et al. 2023

IJMS

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A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus.

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Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Yocca,

Platts,

Alger

et al. 2023

Horticulture Research

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Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

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Phylogeny problems of the genus <i>Vaccinium</i> L. and ways to solve them

Cited by 4 publications

References 36 publications

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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