scholarly journals The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6320 ◽  
Author(s):  
Zhen Yang ◽  
Guixi Wang ◽  
Qinghua Ma ◽  
Wenxu Ma ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Molecular Dating ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Genome Variation ◽  
Genome Data ◽  
Chloroplast Genomes

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The 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.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

scholarly journals Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6032 ◽  
Author(s):  
Zhenyu Zhao ◽  
Xin Wang ◽  
Yi Yu ◽  
Subo Yuan ◽  
Dan Jiang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chloroplast Genomes ◽  
The Family ◽  
Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

scholarly journals Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 474 ◽  
Author(s):  
Dong-Mei Li ◽  
Chao-Yi Zhao ◽  
Xiao-Fei Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Species Identification ◽  
Single Copy ◽  
Rrna Genes ◽  
Genome Sequences ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Kaempferia Galanga ◽  
Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

scholarly journals Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6244 ◽  
Author(s):  
Simon Pfanzelt ◽  
Dirk C. Albach ◽  
K. Bernhard von Hagen
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Sequence Comparisons ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

scholarly journals Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Xu ◽  
Chen Liu ◽  
Yun Song ◽  
Mingfu Li
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

scholarly journals Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu(Former Corresponding Author) ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu(New Corresponding Author)
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily through phylogenetic analysis based on rDNA sequences. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). The phylogenetic relationships among families in order Chaetophorales remain unclear. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales . Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions: chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

scholarly journals The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

2021 ◽  
Vol 51 (3) ◽  
pp. 326-331
Author(s):  
Sung-Dug OH ◽  
Seong-Kon LEE ◽  
Doh-Won YUN ◽  
Hyeon-Jin SUN ◽  
Hong-Gyu KANG ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Intraspecific Variations

The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

scholarly journals Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

2019 ◽  
Vol 20 (23) ◽  
pp. 5940
Author(s):  
Xinbo Pang ◽  
Hongshan Liu ◽  
Suran Wu ◽  
Yangchen Yuan ◽  
Haijun Li ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Species Identification ◽  
Genome Sequence ◽  
Dna Barcode ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Quercus Species ◽  
Chloroplast Genome Sequence

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

scholarly journals Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae

2021 ◽  
Vol 12 ◽  
Author(s):  
Yike Luo ◽  
Jian He ◽  
Rudan Lyu ◽  
Jiamin Xiao ◽  
Wenhe Li ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Arrangement ◽  
Genome Sequences ◽  
Inverted Repeat Region ◽  
Complete Chloroplast Genome ◽  
Evening Primrose ◽  
Chloroplast Genomes ◽  
The Family

The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.

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