The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria

Jiang, Dan; Zhao, Zhenyu; Zhang, Teng; Zhong, Wenhao; Liu, Chunsheng; Yuan, Qingjun; Huang, Luqi

doi:10.3390/genes8090227

Cited by 79 publications

(67 citation statements)

References 51 publications

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“…Furthermore, these cpSSRs are rich in thymine or adenine repeats, but rarely contains guanine or cytosine repeats. Similar findings are also discovered in the cpSSRs of other plant taxa such as Scutellaria (Jiang et al, 2017), Salvia (Qian et al, 2013) and Juglans (Hu et al, 2017). These newly developed repeats and SSRs would be helpful for detecting genetic polymorphisms at population level and assessing distantly related evolutionary relationships within Betulaceae.…”

Section: Chloroplast Genome Variation and Evolutionsupporting

confidence: 66%

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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Section: Chloroplast Genome Variation and Evolutionsupporting

confidence: 66%

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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“…By contrast, there were more mutational events (SNPs and indels) in Eucommia ulmoides [47] and Scutellaria baicalensis [48]. There were 75 SNPs and 80 indels in two different individuals of E. ulmoides [47], 25 SNPs and 29 indels between the two S. baicalensis genotypes [48]. These 23 indels and 20 SNPs could be used for identification of different sources of A. oxyphylla.…”

Section: Interspecific Analyses Of Alpinia Chloroplast Genomesmentioning

confidence: 95%

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

Zhu

et al. 2020

Plants

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Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248–87,667 bp), a small single copy (SSC, 15,306–18,295 bp) and a pair of inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.

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“…Most protein-coding genes (83 or 81 genes) have been used for phylogenetic analyses and have proven to be effective in resolving difficult phylogenetic relationships [ 16 – 18 ]. Noncoding regions are most likely to evolve faster than coding regions in the chloroplast genome, and, therefore, these mutation “hot spots” have been used to identify species and clarify relationships at lower taxonomic levels [ 19 – 23 ].…”

Section: Introductionmentioning

confidence: 99%

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

Cao

Jiang

Zhao

et al. 2018

BioMed Research International

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Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

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The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria

Cited by 79 publications

References 51 publications

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

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

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

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