scholarly journals The complete mitogenome sequence of the coral lily (Lilium pumilum) and the Lanzhou lily (Lilium davidii) in China

2020 ◽  
Vol 15 (1) ◽  
pp. 1060-1067
Author(s):  
Xiangying Qi ◽  
Kaiqi Wang ◽  
Liping Yang ◽  
Zhenshan Deng ◽  
Zhihong Sun
Keyword(s):  
Phylogenetic Tree ◽  
Higher Plants ◽  
Core Protein ◽  
Protein Coding ◽  
Reading Frame ◽  
Intergenic Spacers ◽  
Additional Information ◽  
Mitogenome Sequence ◽  
Complete Mitogenome ◽  
Lilium Davidii

AbstractBackgroundThe mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton).MethodsGenomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed.ResultsThe mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100).ConclusionsL. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.

scholarly journals The Complete Mitochondrial Genome of Critically Endangered Hangul (Cervus Hanglu Hanglu) and Its Comparison With the Other Red Deer

2021 ◽  
Author(s):  
Prabhaker Yadav ◽  
Ajit Kumar ◽  
Neha Yadav ◽  
Sandeep Kumar Gupta
Keyword(s):  
Red Deer ◽  
Synonymous Codon ◽  
Indian Subcontinent ◽  
Complete Mitochondrial Genome ◽  
Synonymous Codon Usage ◽  
Critically Endangered ◽  
Trna Genes ◽  
Intergenic Spacers ◽  
Mitogenome Sequence ◽  
Complete Mitogenome

Abstract Background: Hangul (Cervus hanglu hanglu) or Kashmiri stag belongs to the family Cervidae and is only surviving red deer in the Indian subcontinent. Its complete mitogenome sequence is lacking in the open database for further phylogenetic inferences.Methods and results: We sequenced and characterized the first complete mitogenome of Hangul, which was 16,354 bp in length. It was compared with other red deer subspecies. We observed eight pairs of overlapping genes and 15 intergenic spacers in between the mitochondrial regions. Relative synonymous codon usage (RSCU) for the 13 PCGs of Hangul was consisting of 3597 codons (excluding stop codons). We observed a highest frequency for leucine (11.75%) and the lowest for tryptophan amino acid (1.12%) in 13 PCGs of Hangul. All the tRNA genes showed a typical secondary cloverleaf arrangement, excluding tRNA-Ser in which dihydrouridine arm did not form a stable structure. Conclusions: The Bayesian inference phylogenetic tree indicated that Hangul clustered within the Tarim deer group (C. h. yarkandensis) and closed to C. e. hippelaphus, which formed the western clade. Besides, the subspecies of C. nippon and C. canadensis clustered together and formed an eastern clade. The finding was supported by the mean pairwise genetic distance based on both complete mitogenome and 13 PCGs. The comparative study of the Hangul mitogenome with other red deer provides crucial information for understanding the evolutionary relationships. It offers a valuable resource for conserving this critically endangered cervid with a limited distribution range.

scholarly journals Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning

ZooKeys ◽  
2018 ◽  
Vol 793 ◽  
pp. 1-14
Author(s):  
Wentao Niu ◽  
Shuangen Yu ◽  
Peng Tian ◽  
Jiaguang Xiao
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Molecular Data ◽  
Start Codon ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Genome Data ◽  
Mitogenome Sequence ◽  
Complete Mitogenome ◽  
First Time

Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coralEchinophylliaaspera(Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows thatE.asperaclustered closely withSclerophylliamaxima(Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome ofE.asperaprovides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

Complete mitogenome of Psorodonotus venosus (Orthoptera, Tettigoniidae; Tettigoniinae): Short intergenic spacers shorten the total genome

Zootaxa ◽  
2019 ◽  
Vol 4614 (3) ◽  
pp. 498
Author(s):  
UĞUR KARŞI ◽  
BATTAL ÇIPLAK
Keyword(s):  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Data Bases ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Total Length ◽  
Evolutionary Studies ◽  
Complete Mitogenome ◽  
Generation Sequencing

Mitogenomes are popular sources of data in evolutionary studies. By development of next generation sequencing the number of total mitogenome in data bases rapidly increased. However, there is still a limited number of total mitogenome known from species of Tettigoniinae. This paper aims to describe the total mitogenome of Psorodonotus venosus (Orthoptera, Tettigoniidae; Tettigoniinae) obtained by NGS reads. The total mitogenome is 15836-15845 bp and consists of 13 protein coding genes (PCG), 22 tRNA genes, two rRNA genes and an AT rich control region as in other metazozans. The mitogenome is AT skewed with 69.5% AT percentage. The genes are ordered as in pancrustacean. Total length of PCGs is 11229 bp, the start codon for all fits ATN pattern and stop codons are incomplete T-- / TA- and rarely complete TAA. Total length of 22 tRNA genes is 1447 bp and their anticodons are identical to other members of Tettigonioidea. The mitogenome contains 12 overlapping regions constituting 41 bp in total. Of these 12 overlapping regions those between trnW-trnC, atp6-atp8, nad4-nad4L, nad6 –cytb and atp6-cox3 gene pairs seem to be conserved. The total length of seven noncoding intergenic spacers is 46 bp. We concluded that P. venosus is one of the species with short mitogenome amongst Tettigonioidea because of limited number and length of noncoding intergenic spacers. 

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 Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

scholarly journals The complete mitogenome sequence of the hawk moth, Theretra latreillii subsp. lucasii (Lepidoptera: Sphingidae) from Zhejiang Province, China

2021 ◽  
Vol 6 (7) ◽  
pp. 1880-1882
Author(s):  
Qiaoying Lu ◽  
Hongwei Yao ◽  
Jinming Zhang ◽  
Hongxing Xu ◽  
Caiying Jiang
Keyword(s):  
Zhejiang Province ◽  
Hawk Moth ◽  
Mitogenome Sequence ◽  
Complete Mitogenome

scholarly journals Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Keiko Tanaka ◽  
Takashi Shiina ◽  
Taketeru Tomita ◽  
Shingo Suzuki ◽  
Kazuyoshi Hosomichi ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Close Relation ◽  
Rrna Genes ◽  
Gill Slit ◽  
Mtdna Sequences ◽  
Protein Coding ◽  
Bayesian Phylogenetic Analysis ◽  
Extant Species ◽  
Complete Mitogenome ◽  
Cartilaginous Fishes

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi,Chlamydoselachus anguineus(frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved asChlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus,H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

scholarly journals Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
T. M. Porter ◽  
M. Hajibabaei
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Dna Barcoding ◽  
Profile Analysis ◽  
Hidden Markov ◽  
Open Reading Frame ◽  
Protein Coding ◽  
Reading Frame ◽  
Frame Length ◽  
Open Reading Frame Length

Abstract Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. Results Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. Conclusions Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

The destabilizing elements in the coding region of c-fos mRNA are recognized as RNA

1993 ◽  
Vol 13 (8) ◽  
pp. 5034-5042
Author(s):  
C L Wellington ◽  
M E Greenberg ◽  
J G Belasco
Keyword(s):  
Codon Usage ◽  
Mammalian Cells ◽  
Mrna Decay ◽  
Polypeptide Chain ◽  
Coding Region ◽  
Protein Coding ◽  
Present Evidence ◽  
Reading Frame ◽  
Nascent Polypeptide

The protein-coding region of the c-fos proto-oncogene transcript contains elements that direct the rapid deadenylation and decay of this mRNA in mammalian cells. The function of these coding region instability determinants requires movement of ribosomes across mRNAs containing them. Three types of mechanisms could account for this translational requirement. Two of these possibilities, (i) that rapid mRNA decay might be mediated by the nascent polypeptide chain and (ii) that it might result from an unusual codon usage, have experimental precedent. Here, we present evidence that the destabilizing elements in the c-fos coding region are not recognized in either of these two ways. Instead, the ability of the c-fos coding region to function as a potent mRNA destabilizer when translated in the +1 reading frame indicates that the signals for rapid deadenylation and decay reside in the sequence or structure of the RNA comprising this c-fos domain.

scholarly journals Complete mitochondrial genome of Manis pentadactyla pentadactyla (Mammalia: Pholidota), an endemic subspecies of Chinese pangolin: mitogenome characterisation and phylogenetic implications

2021 ◽  
Vol 9 ◽  
Author(s):  
Nick Sun ◽  
Chi-Chun Huang ◽  
Yu-Wei Tseng ◽  
Tulshi Laxmi Suwal ◽  
Meng-Jou Chi ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Future Research ◽  
Lineage Sorting ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Manis Pentadactyla ◽  
Complete Mitogenome ◽  
Over Exploitation

The Chinese pangolin Manis pentadactyla is critically endangered because of over-exploitation and illegal trafficking and includes three subspecies. However, the taxonomic status of the three subspecies of the Chinese pangolin has not been well resolved, which impedes regional conservation and illegal trade traces. In this study, the complete mitogenome sequence of M. p. pentadactyla, an endemic subspecies of the Chinese pangolin in Taiwan, was determined. The complete mitogenome of M. p. pentadactyla is 16,570 base pairs (bp) in length with 13 protein-coding genes (PCG), 23 transfer RNAs (tRNAs), two ribosomal RNAs and a 1164 bp control region. The overall base composition of the genome showed a slight A + T bias (59.9%), positive AT skew (0.1515) and negative GC skew (-0.3406), which is similar to that of other pangolins. All PCGs started with a typical ATN codon and all tRNAs were typical cloverleaf-shaped secondary structures, except for tRNA-Ser(GCU). Phylogenetic analysis indicated a monophyletic relationship for M. p. pentadactyla and M. p. aurita and was monophyletic for M. p. pentadactyla, but paraphyletic for M. p. aurita. The paraphyly of M. p. aurita resulted from an incomplete lineage sorting. This study enriched the mitogenome database of the Chinese pangolin and the molecular information obtained should be very useful for future research on mitogenome evolution and genetic diversification in M. pentadactyla.

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