Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species

Yang, Zhen; Zhao, Tengteng; Ma, Qinghua; Liang, Lisong; Wang, Guixi

doi:10.3389/fpls.2018.00927

Cited by 58 publications

(48 citation statements)

References 77 publications

(81 reference statements)

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“…The cp genomes of most angiosperms are validated to contain approximately 130 genes, of which about 20 genes have two copies in two IRs, leaving the rest 110 being unique genes (Mader et al, 2018;Hu et al, 2017;Xu et al, 2017;Yang et al, 2018). Our annotations are similar to those reported above.…”

Section: Chloroplast Genome Variation and Evolutionsupporting

confidence: 76%

“…In order to evaluate the sequence divergence of Betulaceae cp genomes, we randomly selected six of the available Betulaceae species (one representative for each of the six genera), including three cp genomes we reported here plus the cp genomes of Carpinus tientaiensis (KY174338), Betula nana (KX703002), and Ostrya rehderiana (KT454094). Based on previous studies, the contraction and expansion of IR regions could bring about the structure variation and length change of cp genomes (Nazareno et al, 2015;Yang et al, 2018). Thus, we performed a comparative analysis to test the variation in the IR/SC junctions among Betulaceae cp genomes.…”

Section: Comparative Analysis and Sequence Divergencementioning

confidence: 99%

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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: 76%

Section: Comparative Analysis and Sequence Divergencementioning

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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“…In our study, both the results from the mVISTA analysis and the nucleotide variability (pi) assessment showed that numerous divergence hotspot regions are primarily situated in the SCs of the cp genome and that more variable sites are located in intergenic regions than in coding genes, and these can be directly utilized for the development of new molecular markers for research on Quercus species identification and taxonomy. Among these divergence hotspot regions, trnH-psbA has already been selected as a suitable barcode for plants [40,73], as have rbcL-accD, trnS-trnG [74], ndhF [40,75], ycf1 [69,76], accD [67,77], trnG-trnR [78] and trnK-rps16 [79]. In this study, the ycf1, ndhF and accD genes were found to be optimal genetic markers based on their high substitution variability, repeat sequence diversity and SSC/IR junction length variability.…”

Section: Discussionmentioning

confidence: 91%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Chang

Liu

et al. 2019

Forests

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Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant.No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex , Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus. single-copy regions (LSC and SSC) [4,5]. Due to its uniparental inheritance, highly conserved structure, general lack of recombination and small effective population size, the analysis of cp DNA has been deemed a useful method for evolution research and the exploration of plant systematics [6][7][8][9]. In fact, the availability of sufficient data on cp genomes is crucial for phylogenetic relationship reconstruction, i.e., the assessment of relationships within angiosperms [10][11][12], the identification of members of Pinaceae [13] and Pinus [14], and adequate comparisons, i.e., cp genomes from sister species [15] and possibly multiple individuals [16]. At present, approximately 3000 plastid genomes of Eukaryota are shareable in the National Center for Biotechnology Information database (NCBI; Available online: https: //www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=plastid&taxid=2759&sort=Genome) due to improvements in sequencing technologies. In addition, molecular genetic methodologies based on nuclear and organellar genomes are crucial for conservation studies [17], particularly the con...

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“…Recently, phylogenetic analysis of whole chloroplast genomes was suggested as an alternative to provide better resolution for species designation [ 10 , 11 ]. In support of this, consolidation of alignments for the majority of genes in a plastid genome has been successfully used for building species trees in a number of instances [ 12 – 14 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae)

et al. 2020

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Iris is one of the largest genera in the family Iridaceae , comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris , is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea , have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup ( Sisyrinchium angustifolium ), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species.

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Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species

Cited by 58 publications

References 77 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 Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae)

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