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

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.

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

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.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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

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.

scholarly journals Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Li-Shang Dai ◽  
Bao-Jian Zhu ◽  
Yue Zhao ◽  
Cong-Fen Zhang ◽  
Chao-Liang Liu
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Relationships ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Lepidopteran Insects ◽  
Usage Analysis ◽  
Mitochondrial Trna Genes ◽  
Cloverleaf Structure

Abstract In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) − rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily.

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

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7830 ◽  
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.

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

ZooKeys ◽  
2018 ◽  
Vol 790 ◽  
pp. 127-144 ◽  
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.

scholarly journals Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

2020 ◽  
Author(s):  
Yan Cheng ◽  
Xiaoxue He ◽  
S. V. G. N. Priyadarshani ◽  
Yu Wang ◽  
Li Ye ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Sandy Beaches ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Landscape Plant ◽  
Suaeda Glauca ◽  
Mt Genome ◽  
Mitochondria Genome

Abstract Background Suaeda glauca is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also a beautiful landscape plant with high development prospects and scientific research value. The S. glauca chloroplast genome has recently been reported; however, the mitochondria genome is still unexplored. Results This study assembled the mitochondria genome and annotated the mitochondrial genes of S. glauca based on the Pacbio long reads. The circular mitochondrial genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (27.96%), T (28.01%), C (21.64%), G (21.64%). S. glauca mt genome has 51 genes, including 26 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Phylogenetic analysis with common genes of 28 species resulted in similar morphological classification. Conclusions As a Chenopodiaceae species, S. glauca mt genome will provide insights into the missing pieces in the evolution of sex determination and improve genomic breeding in the future.

A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

2014 ◽  
Vol 35 (3) ◽  
pp. 331-343 ◽  
Author(s):  
Yongmin Li ◽  
Huabin Zhang ◽  
Xiaoyou Wu ◽  
Hui Xue ◽  
Peng Yan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar)

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 739-747 ◽  
Author(s):  
T. HUYSE ◽  
L. PLAISANCE ◽  
B. L. WEBSTER ◽  
T. A. MO ◽  
T. A. BAKKE ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Ribosomal Rna ◽  
Trna Gene ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mt Genome

SUMMARYIn the present study, we describe the complete mitochondrial (mt) genome of the Atlantic salmon parasite Gyrodactylus salaris, the first for any monogenean species. The circular genome is 14 790 bp in size. All of the 35 genes recognized from other flatworm mitochondrial genomes were identified, and they are transcribed from the same strand. The protein-coding and ribosomal RNA (rRNA) genes share the same gene arrangement as those published previously for neodermatan mt genomes (representing cestodes and digeneans only), and the genome has an overall A+T content of 65%. Three transfer RNA (tRNA) genes overlap with other genes, whereas the secondary structure of 3 tRNA genes lack the DHU arm and 1 tRNA gene lacks the TΨC arm. Eighteen regions of non-coding DNA ranging from 4 to 112 bp in length, totalling 278 bp, were identified as well as 2 large non-coding regions (799 bp and 768 bp) that were almost identical to each other. The completion of the mt genome offers the opportunity of defining new molecular markers for studying evolutionary relationships within and among gyrodactylid species.

scholarly journals Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus

2021 ◽  
Vol 11 ◽  
Author(s):  
Kaihui Zhao ◽  
Lianqiang Li ◽  
Hong Quan ◽  
Junbo Yang ◽  
Zhirong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Evolutionary Analysis ◽  
Classification Problems ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Mutational Hotspots

Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.

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