The complete chloroplast genome sequence of sugar beet (<i>Beta vulgaris</i>ssp.<i>vulgaris</i>)

Han, Li; Cao, Hua; Cai, Yanfei; Wang, Jihua; Qu, S.; Huang, Xing-Qi

doi:10.3109/19401736.2014.883611

Cited by 27 publications

(19 citation statements)

References 10 publications

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“…vulgaris ) (Li et al, 2014). The size of the S. oleracea cp genome (150,725 bp) (Schmitz-Linneweber et al, 2001) is intermediate (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…vulgaris (GenBank accession number KJ081864.1, Beta vulgaris subsp. vulgaris ) (Li et al, 2014), two closely related species in the Amaranthaceae family, were downloaded from GenBank databases (www.ncbi.nlm.nih.gov). These were used for comparison with the complete cp genomes of HA and HP.…”

Section: Methodsmentioning

confidence: 99%

“…vulgaris ) from members of the Amaranthaceae family (Li et al, 2014; Schmitz-Linneweber et al, 2001). However, the determination of the cp genome from Haloxylon plants is of further significance for potentially enhancing our understanding of their adaptability to severe desert environmental conditions, and their genomic evolution within the Amaranthaceae.…”

Section: Introductionmentioning

confidence: 99%

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

Dong

et al. 2016

PeerJ

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The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.

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“…vulgaris ) (Li et al, 2014). The size of the S. oleracea cp genome (150,725 bp) (Schmitz-Linneweber et al, 2001) is intermediate (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Dong

et al. 2016

PeerJ

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“…They showed a typical quadripartite structure similar to that of the cp genomes of most land plants (Li et al, 2014;Wang et al, 2013), with large and small single copy regions (LSC and SSC) separated by two copies of inverted repeats (IRa and IRb). The entire gene contents and relative positions of 131 individual genes (86 PCGs, eight rRNA, and 37 tRNA genes) were identical between the two C. sativa cp genomes.…”

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confidence: 93%

Two complete chloroplast genome sequences of Cannabis sativa varieties

Seo

Lee

et al. 2015

Mitochondrial DNA Part A

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In this study, we determined the complete chloroplast (cp) genomes from two varieties of Cannabis sativa. The genome sizes were 153,848 bp (the Korean non-drug variety, Cheungsam) and 153,854 bp (the African variety, Yoruba Nigeria). The genome structures were identical with 131 individual genes [86 protein-coding genes (PCGs), eight rRNA, and 37 tRNA genes]. Further, except for the presence of an intron in the rps3 genes of two C. sativa varieties, the cp genomes of C. sativa had conservative features similar to that of all known species in the order Rosales. To verify the position of C. sativa within the order Rosales, we conducted phylogenetic analysis by using concatenated sequences of all PCGs from 17 complete cp genomes. The resulting tree strongly supported monophyly of Rosales. Further, the family Cannabaceae, represented by C. sativa, showed close relationship with the family Moraceae. The phylogenetic relationship outlined in our study is well congruent with those previously shown for the order Rosales.

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“…With the accumulation of angiosperm cp genomes, comparative genomics and phylogenomics of closely related cp genomes are very useful for grasping the genome evolution regarding structure variations, nucleotide substitutions, and gene losses (Hu et al, 2017;Raman et al, 2016;Barrett et al, 2016). Meanwhile, lots of high-resolution genetic markers, such as intergenic spacer (IGS) fragments , simple sequence repeats (SSRs) , single nucleotide polymorphisms (SNPs) (Li et al, 2014), and repeated sequences (Provan et al, 2001) were identified across the cp genomes and applied for multi-aspect studies in different plant taxa.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography (v0.1)"

2019

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Background. Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. Chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods. Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results. Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions. This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae. It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

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The complete chloroplast genome sequence of sugar beet (Beta vulgarisssp.vulgaris)

Cited by 27 publications

References 10 publications

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

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

Two complete chloroplast genome sequences of Cannabis sativa varieties

Peer Review #2 of "The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography (v0.1)"

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