scholarly journals The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content Within Poaceae

2019 ◽  
Author(s):  
Nathan D Hall ◽  
Hui Zhang ◽  
Jeffrey P Mower ◽  
J Scott McElroy ◽  
Leslie R Goertzen
Keyword(s):  
Mitochondrial Genome ◽  
Finger Millet ◽  
Size Structure ◽  
Gene Content ◽  
Protein Coding ◽  
Eleusine Indica ◽  
Organelle Genomes ◽  
Genomic Gene ◽  
Mt Genome

Abstract Plant mitochondrial (mt) genome assembly provides baseline data on size, structure and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The mitochondrial genome for Eleusine indica (Poaceae: goosegrass) is comprehensibly analyzed here, providing key reference data for an economically significant invasive species that is also the maternal parent of the allotetraploid crop Finger millet (Eleusine coracana). The assembled E. indica genome contains 33 protein coding genes, 6 rRNA subunits, 24 tRNA, 8 large repetitive regions 15 kb of transposable elements across a total of 520,691 bp. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4 and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of available publicly available data. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade.

Characterization of the complete mitochondrial genome of Ortleppascaris sinensis (Nematoda: Heterocheilidae) and comparative mitogenomic analysis of eighteen Ascaridida nematodes

2017 ◽  
Vol 92 (3) ◽  
pp. 369-378 ◽  
Author(s):  
J.H. Zhao ◽  
G.J. Tu ◽  
X.B. Wu ◽  
C.P. Li
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Molecular Ecology ◽  
Protein Coding ◽  
Intestinal Nematode ◽  
The Family ◽  
Polymerase Chain ◽  
Mt Genome

AbstractOrtleppascaris sinensis (Nematoda: Ascaridida) is a dominant intestinal nematode of the captive Chinese alligator. However, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. In this study, the complete mitochondrial (mt) genome sequence of O. sinensis was first determined using a polymerase chain reaction (PCR)-based primer-walking strategy, and this is also the first sequencing of the complete mitochondrial genome of a member of the genus Ortleppascaris. The circular mitochondrial genome (13,828 bp) of O. sinensis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes, but lacked the ATP synthetase subunit 8 gene. Finally, phylogenetic analysis of mtDNAs indicated that the genus Ortleppascaris should be attributed to the family Heterocheilidae. It is necessary to sequence more mtNDAs of Ortleppascaris nematodes in the future to test and confirm our conclusion. The complete mitochondrial genome sequence of O. sinensis reported here should contribute to molecular diagnosis, epidemiological investigations and ecological studies of O. sinensis and other related Ascaridida nematodes.

scholarly journals Characterization of the Complete Mitochondrial Genome of Fischoederius elongatus Derived from Cows in Shanghai, China

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Zhaoqing Han ◽  
Kun Li ◽  
Houqiang Luo ◽  
Muhammad Shahzad ◽  
Khalid Mehmood
Keyword(s):  
Amino Acids ◽  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Parasite Species ◽  
Codon Position ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Rna Genes

A study was conducted to reveal the characterization of the complete mitochondrial genome of Fischoederius elongatus derived from cows in Shanghai, China. Results indicated that the complete mt genome of F. elongatus was 14,288 bp and contained 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6, and cytb), 22 transfer RNA genes, and two ribosomal RNA genes (l-rRNA and s-rRNA). The overall A + T content of the mt genome was 63.83%, and the nucleotide composition was A (19.83%), C (9.75%), G (26.43%), and T (44.00%). A total of 3284 amino acids were encoded by current F. elongatus isolate mt genome, TTT (Phe) (9.84%) and TTG (Leu) (7.73%) codon were the most frequent amino acids, whereas the ACC (Thr) (0.06%), GCC (Ala) (0.09%), CTC (Leu) (0.09%), and AAC (Asn) (0.09%) codon were the least frequent ones. At the third codon position of F. elongatus mt protein genes, T (50.82%) was observed most frequently and C (5.85%) was the least one. The current results can contribute to epidemiology diagnosis, molecular identification, taxonomy, genetic, and drug development researches about this parasite species in cattle.

Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome

Genome ◽  
2010 ◽  
Vol 53 (4) ◽  
pp. 285-301 ◽  
Author(s):  
Wannes Dermauw ◽  
Bartel Vanholme ◽  
Luc Tirry ◽  
Thomas Van Leeuwen
Keyword(s):  
Mitochondrial Genome ◽  
Phytoseiulus Persimilis ◽  
Predatory Mite ◽  
12S Rrna ◽  
Closely Related Species ◽  
Protein Coding ◽  
Hybridization Data ◽  
Metaseiulus Occidentalis ◽  
Standard Set ◽  
Mt Genome

In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) — which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms — the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.

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.

scholarly journals Characterization of the complete plastomes of two flowering epiparasites (Phacellaria glomerata and P. compressa, Santalaceae, Santalales): gene content, organization and plastome degradation

2019 ◽  
Author(s):  
Xiaorong Guo ◽  
Changkun Liu ◽  
Hengchang Wang ◽  
Guangfei Zhang ◽  
Hanjing Yan ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Growth Form ◽  
Size Structure ◽  
General Pattern ◽  
Gene Content ◽  
Evolutionary Pathway ◽  
Plant Parasite ◽  
Content Organization ◽  
Plastome Degradation

Abstract Backgrounds: The transition to a heterotrophic lifestyle triggers reductive evolution of plastid genome (plastome) in both photosynthetic and non–photosynthetic parasites. A plant parasite parasitizing another plant parasite is referred to as epiparasitism, which is extremely rare in angiosperms. In despite of the particularly special lifeform of epiparasitic plants, their plastomes have not been characterized to date. Sequending such plastomes may enable new insights into the evolutionary pathway of plastome degradation associated with parasitism. Results: In this study, we generated complete plastomes of Phacellaria compressa and P. glomerata (Santalaceae, Santalales) through Illumina shotgun sequencing. Plastome assembly and comparison indicated that plastomes of both species exhibit the quadripartite structure typical of angiosperms, and that they possess similar size, structure, gene content, and arrangement of genes to other hemiparasites in Santalales, especially to those hemiparasites in Santalaceae. The plastomes of P. compressa and P. glomerata were characterized by the functional loss of plastid–encoded NAD(P)H–dehydrogenase and infA genes, which strongly coincides with the general pattern of plastome degradation observed in Santalales hemiparasites. Conclusion: Our study demonstrates that the shift to epiparasitism and reduced vegetative bodies in P. compressa and P. glomerata do not appear to cause any unique plastome degradation compared with their closely related hemiparasites. The epiparasitic lifestyle or an endophytic growth form observed in these two epiparasites may have limited impact on the reductive modification of their plastomes.

scholarly journals Complete Mitochondrial Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

2021 ◽  
Author(s):  
Yingfeng Niu ◽  
Chengwen Gao ◽  
Jin Liu
Keyword(s):  
Mitochondrial Genome ◽  
Genomic Structure ◽  
Mangifera Indica ◽  
Gene Content ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

scholarly journals Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6866 ◽  
Author(s):  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Zhenyi Li ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A New Species ◽  
High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

scholarly journals The Whole Genome Assembly and Comparative Genomic Research ofThellungiella parvula(Extremophile Crucifer) Mitochondrion

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xuelin Wang ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
Suyun Wei ◽  
Xiaogang Dai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Protein Coding ◽  
Ssr Analysis ◽  
Brassicaceae Species ◽  
Mt Genome ◽  
Rna Genes

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile speciesThellungiella parvula(T. parvula) have been determined with the lengths of 255,773 bp.T. parvulamt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome ofT. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species,T. parvulais related toArabidopsis thalianawhose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

Zootaxa ◽  
2012 ◽  
Vol 3238 (1) ◽  
pp. 23 ◽  
Author(s):  
AIMIN SHI ◽  
HU LI ◽  
XIAOSHUAN BAI ◽  
XUN DAI ◽  
JIAN CHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Gene Arrangement ◽  
Entire Genome ◽  
Protein Coding ◽  
Simple Loop ◽  
Secondary Structure Models ◽  
Mt Genome

The 15528 bp long complete mitochondrial genome (mt-genome) of a flat bug, Aradacanthia heissi Bai, Zhang & Cai,was determined. The entire genome contains typical 37 genes with an A+T content of 74.7%. The gene arrangement dif-fers from that of Drosophila yakuba Burla which is considered the representative ground pattern for insect mt-genomes,as the results of inversion of tRNAIle - tRNAGln and tRNACys - tRNATrp . All protein-coding genes (PCGs) use standard initia-tion codons (methionine and isoleucine), except COI which starts with TTG. Three of the 13 PCGs harbor the incompletetermination codon. Meanwhile, opposite CG-skew tendency occurs on the nucleotide composition and codon usage andthis tendency is also reflected on the J-strand and N-strand of PCGs. All tRNAs can fold into classic clover-leaf structure,whereas the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomalRNA genes of A. heissi are predicted and similar to those proposed for other insects. The control region is located betweensrRNA and tRNAGln with 81.5% A+T content, which was the most A+T-rich region of the mt-genome and four 68 bp tan-dem repeat units were found in this region. Phylogenetic analyses of available species of Pentatomomorpha showed Ara-doidea and the Trichophora are sister groups that bolstered the mainstream hypothesis, and provide the evidence for the feasibility of mt-genome data to resolve relationships at the subfamily level in Aradidae.

scholarly journals Preliminary Characterization of Mitochondrial Genome ofMelipona scutellaris, a Brazilian Stingless Bee

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Manuella Souza Silverio ◽  
Vinícius de Rezende Rodovalho ◽  
Ana Maria Bonetti ◽  
Guilherme Corrêa de Oliveira ◽  
Sara Cuadros-Orellana ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Dna Barcode ◽  
Illumina Miseq ◽  
Stingless Bee ◽  
Protein Coding ◽  
Accurate Picture ◽  
Melipona Bicolor ◽  
History Of

Bees are manufacturers of relevant economical products and have a pollinator role fundamental to ecosystems. Traditionally, studies focused on the genusMeliponahave been mostly based on behavioral, and social organization and ecological aspects. Only recently the evolutionary history of this genus has been assessed using molecular markers, including mitochondrial genes. Even though these studies have shed light on the evolutionary history of theMeliponagenus, a more accurate picture may emerge when full nuclear and mitochondrial genomes ofMeliponaspecies become available. Here we present the assembly, annotation, and characterization of a draft mitochondrial genome of the Brazilian stingless beeMelipona scutellarisusingMelipona bicoloras a reference organism. Using Illumina MiSeq data, we achieved the annotation of all protein coding genes, as well as the genes for the two ribosomal subunits (16S and 12S) and transfer RNA genes as well. Using the COI sequence as a DNA barcode, we found thatM. cramptoniis the closest species toM. scutellaris.

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