The complete chloroplast genome of Vaccinium fragile (Vacciniaceae), a shrub endemic to China

Abstract

Vaccinium fragile , an endemic species in China, is a plant of the family Vacciniaceae. It is an evergreen shrubby tree distributed in Sichuan, Guizhou, Yunnan, and Tibet province of China. The chloroplast (cp) genome of V. fragile is 169,480 bp in size containing 123 unique genes, including 8 rRNA genes, 38 tRNA genes, and 77 protein-coding genes (PCGs). Phylogenetic analysis exhibited that both V. macrocarpon and V. fragile were phylogenetically closer to Arbutus unedo than other taxa in this study.

Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops

“…Since the first Vaccinium chloroplast DNA sequence was published in 2013 22 , next-generation sequencing technologies have enabled the assembly of plastomes for additional species in this genus, making ten Vaccinium cpDNAs available to date [22][23][24][25][26][27][28][29] . Here, we performed de novo assembly of the plastomes of five additional Vaccinium samples, focusing specifically on crops of economic importance (four cultivated blueberry types and bilberry).…”

“…Moreover, the genetic properties of chloroplasts (i.e., uniparental inheritance, haploid, and nonrecombinant nature) can simplify phylogenetic reconstructions when dealing with mixed-ploidy species, and facilitate the usage of their polymorphic sites as molecular markers. However, only a few Vaccinium chloroplast genomes have been published so far, with most of these studies reporting only the plastome assembly, without performing comparative analyses [22][23][24][25][26][27][28][29] . Moreover, organellar genomes of horticultural plants are overall underrepresented in databases 30 .…”

Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

“…Since the first Vaccinium chloroplast DNA sequence was published in 2013 [21], nextgeneration sequencing technologies have enabled the assembly of plastomes for additional species in this genus, making nine Vaccinium cpDNAs available to date [21][22][23][24][25][26][27]. Here, we performed de novo assembly of the plastomes of five additional Vaccinium species, including the four most important cultivated blueberry types and bilberry.…”

“…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).…”

“…Whole chloroplasts can provide more sequence-based polymorphisms, and its genetic properties (i.e., uniparental inheritance, haploid, and nonrecombinant nature) can simplify phylogenetic reconstructions when dealing with mixed-ploidy species. However, only a few Vaccinium chloroplast genomes have been published so far, with most of these studies reporting only the plastome assembly, without performing comparative analyses [21][22][23][24][25][26][27]. Moreover, organellar genomes of horticultural plants are overall underrepresented in databases [28].…”