scholarly journals Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoidEutreptiella pomquetensis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3725 ◽  
Author(s):  
Nadja Dabbagh ◽  
Matthew S. Bennett ◽  
Richard E. Triemer ◽  
Angelika Preisfeld
Keyword(s):  
Chloroplast Genome ◽  
Green Algae ◽  
Gene Clusters ◽  
Single Copy ◽  
Protein Coding ◽  
Group Iii ◽  
Chloroplast Genomes ◽  
Plant Chloroplast ◽  
Intron Content ◽  
High Level

BackgroundOver the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome ofEutreptiella pomquetensis, and the spread and peculiarities of introns.MethodsTheEtl. pomquetensiscpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, includingPyramimonas parkeae.Results and DiscussionWith about 130,561 bp the chloroplast genome ofEtl. pomquetensis, a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions inEtl. pomquetensiswas completely different from those observed in green algae and plants. The gene composition ofEtl. pomquetensiswas extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not toP. parkeae. Furthermore, the cpGenome ofEtl. pomquetensiswas unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns ofEtl. pomquetensisshowed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III introns are degenerated group II introns and evolved later.

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 The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis

2007 ◽  
Vol 12 (4) ◽  
Author(s):  
Wojciech Pląder ◽  
Yasushi Yukawa ◽  
Masahiro Sugiura ◽  
Stefan Malepszy
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Trna Genes ◽  
Inverted Repeat Region ◽  
Cucumis Sativus L ◽  
Stem Loop ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Trna Species ◽  
Rrna Species

AbstractThe complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.

scholarly journals Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis—“Wild Plants with a Tiny Population”—and Three Other Pyrus Species

2018 ◽  
Vol 19 (10) ◽  
pp. 3262 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Longfei Li ◽  
Lijuan Gao ◽  
Jintao Xu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Population Decline ◽  
Gc Content ◽  
Single Copy ◽  
Wild Plants ◽  
Similar Degree ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
History Of

Pyrus hopeiensis is a valuable wild resource of Pyrus in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the “wild plants with a tiny population” in China. To date, few studies have been conducted on P. hopeiensis. This paper offers a systematic review of P. hopeiensis, providing a basis for the conservation and restoration of P. hopeiensis resources. In this study, the chloroplast genomes of two different genotypes of P. hopeiensis, P. ussuriensis Maxin. cv. Jingbaili, P. communis L. cv. Early Red Comice, and P. betulifolia were sequenced, compared and analyzed. The two P. hopeiensis genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of P. hopeiensis HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of P. hopeiensis HB-2. The lengths of the SSC and IR regions of the two Pyrus genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in P. hopeiensis HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of P. hopeiensis were similar to those of the other three Pyrus species. The IR boundary of the two genotypes of P. hopeiensis showed a similar degree of expansion. To determine the evolutionary history of P. hopeiensis within the genus Pyrus and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera Pyrus and Malus, and the relationship between P. hopeiensis HB-1 and P. hopeiensis HB-2 was the closest.

scholarly journals Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

2021 ◽  
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah . ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Gc Content ◽  
Single Copy ◽  
Phyllanthus Emblica ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family

Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

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 Comparative Chloroplast Genomics in Phyllanthaceae Species

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 403
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Single Copy ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family ◽  
Insight Into ◽  
Small Single Copy

Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, and trees that are mostly distributed in tropical regions. Here, we elucidate the molecular evolution of the chloroplast genome in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference. We de novo assembled the chloroplast genomes of three Phyllanthaceae species, i.e., Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius, and compared them with six other previously reported genomes. All species comprised two inverted repeat regions (size range 23,921–27,128 bp) that separated large single-copy (83,627–89,932 bp) and small single-copy (17,424–19,441 bp) regions. Chloroplast genomes contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, and 4 rRNAs. The deletion/pseudogenization of rps16 genes was found in only two species. High variability was seen in the number of oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions were similar. The transition substitutions were higher in coding sequences than in non-coding sequences. Phylogenetic analysis revealed the polyphyletic nature of the genus Phyllanthus. The polymorphic protein-coding genes, including rpl22, ycf1, matK, ndhF, and rps15, were also determined, which may be helpful for reconstructing the high-resolution phylogenetic tree of the family Phyllanthaceae. Overall, the study provides insight into the chloroplast genome evolution in Phyllanthaceae.

scholarly journals Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

2021 ◽  
Vol 11 ◽  
Author(s):  
Yongtan Li ◽  
Yan Dong ◽  
Yichao Liu ◽  
Xiaoyue Yu ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Evolutionary Relationships ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Cp Genome

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

scholarly journals Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions

2018 ◽  
Author(s):  
Kyoung Su Choi ◽  
Keum Seon Jeong ◽  
Young-Ho Ha ◽  
Kyung Choi
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Repeat Structure ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates

Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

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