The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, IR expansions and phylogenomic implications

Abstract Background: Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandiflorus and S. validus, and carried out a comprehensive comparative analysis.Results: The four Selenicereus plastomes all have a typical quartile structure. The plastome size ranged from 133,146 bp to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the IR regions had undergone a dramatic expansion and formed a previously unreported SC/IR border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Phylogenetic analysis indicated that Hylocereus was nested in Selenicereus.Conclusion: Our study enriches the plastomic resources in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.

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Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

Systematic Botany ◽

10.1600/036364421x16128061189576 ◽

2021 ◽

Vol 46 (1) ◽

pp. 162-174

Author(s):

Ming-Hui Yan ◽

Chun-Yang Li ◽

Peter W. Fritsch ◽

Jie Cai ◽

Heng-Chang Wang

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Signal ◽

Strong Support ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

International Journal of Molecular Sciences ◽

10.3390/ijms21134685 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4685

Author(s):

Zhenhai Li ◽

Min Li ◽

Shannan Xu ◽

Li Liu ◽

Zuozhi Chen ◽

...

Keyword(s):

Divergence Time ◽

Rrna Genes ◽

12S Rrna ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Gc Skew ◽

The Family ◽

Conserved Genes

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

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Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae

PeerJ ◽

10.7717/peerj.7830 ◽

2019 ◽

Vol 7 ◽

pp. e7830 ◽

Cited By ~ 1

Author(s):

Eugeny V. Gruzdev ◽

Vitaly V. Kadnikov ◽

Alexey V. Beletsky ◽

Andrey V. Mardanov ◽

Nikolai V. Ravin

Keyword(s):

Genome Evolution ◽

Plastid Genome ◽

Housekeeping Genes ◽

Parasitic Plants ◽

Rrna Genes ◽

Phylogenetic Position ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Plastid Genome Evolution

Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.

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The complete mitochondrial genome of Orancistrocerus aterrimus aterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

ZooKeys ◽

10.3897/zookeys.790.25356 ◽

2018 ◽

Vol 790 ◽

pp. 127-144 ◽

Cited By ~ 2

Author(s):

Qiao-Hua Zhang ◽

Pan Huang ◽

Bin Chen ◽

Ting-Jing Li

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Translation Termination ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Tandem Repeat Sequences ◽

The Family

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome ofO.a.aterrimusis 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except forcox1using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2,cox3,nad4, andcytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except fortrnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extratrnM2located betweentrnQandnad2and thetrnL2in the upstream ofnad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation betweentrnS1andtrnEgenes only appears in Vespinae, and the translocation oftrnYin Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome ofO.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

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Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

10.21203/rs.3.rs-49270/v3 ◽

2020 ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Dna Barcode ◽

Sequence Divergence ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Hypervariable Regions ◽

Plastid Genomes ◽

Insight Into

Abstract Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis

Scientific Reports ◽

10.1038/s41598-021-93480-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongxia Yang ◽

Wenhui Li ◽

Xiaolei Yu ◽

Xiaoying Zhang ◽

Zhongyi Zhang ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Rrna Genes ◽

Trna Genes ◽

Ribosomal Protein Genes ◽

Protein Coding ◽

Medicinal Value ◽

The Family ◽

Gleditsia Sinensis ◽

Mt Genome ◽

Insight Into

AbstractGleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae.

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Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

BMC Plant Biology ◽

10.1186/s12870-020-02793-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Dna Barcode ◽

Sequence Divergence ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Hypervariable Regions ◽

Plastid Genomes ◽

Insight Into

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca ‘Greizy’, Pilea peperomioides and Pilea serpyllacea ‘Globosa’) and performed comprehensive comparative analysis. Results The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. Conclusion Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj18.390 ◽

2018 ◽

Vol 22 (5) ◽

pp. 524-530 ◽

Cited By ~ 1

Author(s):

M. A. Filyushin ◽

A. M. Mazur ◽

A. V. Shchennikova ◽

Е. Z. Kochieva

Keyword(s):

Comparative Analysis ◽

Rrna Genes ◽

Trna Genes ◽

Vegetable Crops ◽

Structural Elements ◽

Protein Coding ◽

Plastid Genomes ◽

Plastome Evolution ◽

Taxonomic Studies

Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is different: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.

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Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

Frontiers in Genetics ◽

10.3389/fgene.2020.560368 ◽

2020 ◽

Vol 11 ◽

Author(s):

Peninah Cheptoo Rono ◽

Xiang Dong ◽

Jia-Xin Yang ◽

Fredrick Munyao Mutie ◽

Millicent A. Oulo ◽

...

Keyword(s):

Tandem Repeats ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Coding Region ◽

Base Pairs ◽

Protein Coding ◽

Chloroplast Genomes ◽

The Family ◽

Cp Genome

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

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Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae)

Plants ◽

10.3390/plants10010109 ◽

2021 ◽

Vol 10 (1) ◽

pp. 109

Author(s):

Kuan Liu ◽

Rong Wang ◽

Xiu-Xiu Guo ◽

Xue-Jie Zhang ◽

Xiao-Jian Qu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Structure ◽

Single Copy ◽

Rrna Genes ◽

Molecular Evidence ◽

Trna Genes ◽

Protein Coding ◽

Hypervariable Regions ◽

Chloroplast Genomes ◽

Small Single Copy

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.

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