The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Abstract

Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.

Comparative analysis of the complete chloroplast genome sequences in psammophyticHaloxylonspecies (Amaranthaceae)

“…In each of the four Amaranthaceae cp genomes in our analysis, the rpl 2 gene has lost its intron. Some authors have proposed that intron loss is not always a dependable marker of phylogenetic relationships (Millen et al, 2001; Dong et al, 2013b; Raman & Park, 2016), and further study, including the sampling of more taxa, is needed to clarify this issue.…”

“…Each leaf cell of plants contains 1,000–10,000 chloroplasts (cp), which are key organelles for photosynthesis and other biochemical pathways such as the biosynthesis of starch, fatty acids, pigments, and amino acids (Dong et al, 2013b; Raman & Park, 2016). Since the first cp genome of Nicotiana tabacum was sequenced in 1986, around 800 complete cp genome sequences have been made available in the National Center for Biotechnology Information organelle genome database.…”

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

“…The number of tRNA genes and rRNA genes in Juglans was the same as in five Quercus species (Yang et al, 2016). Moreover, the total number of introns in the Juglans Cpg was the same as Quercus rubra (Alexander and Woeste, 2014), Ampelopsis (Raman and Park, 2016), and Saxifragales (Dong et al, 2013). Several lineages of angiosperms have independently lost introns from the ribosomal protein genes rps16, rps12 , and rpl16 (Downie et al, 1991; Downie and Palmer, 1992), including Geraniaceae and Caryophyllales (Logacheva et al, 2008).…”

“…Several lineages of angiosperms have independently lost introns from the ribosomal protein genes rps16, rps12 , and rpl16 (Downie et al, 1991; Downie and Palmer, 1992), including Geraniaceae and Caryophyllales (Logacheva et al, 2008). The five Chinese Juglans species have not lost introns in any of these genes, however, a characteristic they have in common with the woody plant family Vitaceae (Raman and Park, 2016). …”

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

“…Chloroplasts are key organelles in plants for photosynthesis and other biochemical pathways such as the biosynthesis of starch, fatty acids, pigments, and amino acids (Dong et al, 2013, 2016; Raman and Park, 2016). Chloroplast (cp) genome, as one of the three DNA genomes (the other two are nuclear and mitochondrial genomes) in plant body, with uniparental inheritance, has a highly conserved circular DNA arrangement ranging from 115 to 165 kb.…”