The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

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Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽

10.11646/zootaxa.4952.2.7 ◽

2021 ◽

Vol 4952 (2) ◽

pp. 331-353

Author(s):

CHAO YANG ◽

LE ZHAO ◽

QINGXIONG WANG ◽

HAO YUAN ◽

XUEJUAN LI ◽

...

Keyword(s):

Secondary Structure ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Comparative Analyses ◽

Protein Coding Genes ◽

Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

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Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

PeerJ ◽

10.7717/peerj.2786 ◽

2016 ◽

Vol 4 ◽

pp. e2786 ◽

Cited By ~ 18

Author(s):

Siqi Yuan ◽

Yun Xia ◽

Yuchi Zheng ◽

Xiaomao Zeng

Keyword(s):

Next Generation Sequencing ◽

Gene Order ◽

Illumina Miseq ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Gene Rearrangements ◽

Next Generation ◽

Protein Coding ◽

Alignment Errors ◽

Generation Sequencing

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome ofA. chunganensisandQ. boulengeriare typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome ofQ. boulengeriis characterized with a tandem duplication oftrnM. Moreover, we utilize 13 protein-coding genes ofA. chunganensis,Q. boulengeriand other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity ofA. chunganensisandQ. boulengeri. In this work, we provide nearly complete mitochondrial genomes ofA. chunganensisandQ. boulengeri.

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PEMANFAATAN TEKNOLOGI SEKUENSING GENOM UNTUK MEMPERCEPAT PROGRAM PEMULIAAN TANAMAN

Jurnal Penelitian dan Pengembangan Pertanian ◽

10.21082/jp3.v34n4.2015.p159-168 ◽

2016 ◽

Vol 34 (4) ◽

pp. 159

Author(s):

I Made Tasma

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Coding Region ◽

Protein Coding ◽

Snp Chip ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Sumber daya genetik (SDG) tanaman menyediakan materi dasar untuk program pemuliaan tanaman. Namun, baru sebagian kecil (<1%) koleksi SDG yang dimanfaatkan untuk pemuliaan tanaman. Karakterisasi SDG sudah banyak dilakukan dengan menggunakan karakter morfologi, namun metode ini lambat, menyita waktu, dan memerlukan banyak tenaga. Teknologi sekuensing modern menghasilkan peta genom rujukan suatu spesies tanaman yang dapat mempercepat karakterisasi SDG menggunakan teknik next generation sequencing (NGS). Tulisan ini mengulas pemanfaatan teknologi sekuensing genom untuk karakterisasi, proteksi, dan pemanfaatan SDG untuk mempercepat program pemuliaan tanaman. Di Indonesia, teknologi NGS telah dimanfaatkan sejak 2010 untuk resekuensing genom komoditas unggulan nasional seperti kedelai, kakao, jagung, dan cabai merah. Jutaan SNP dan Indel telah diidentifikasi pada setiap komoditas sebagai sumber daya pemuliaan yang bernilai tinggi. Sebagian kecil SNP/Indel tersebut berada pada protein coding region yang potensial untuk penemuan gen-gen unggul. Selain SNP yang diidentifikasi pada semua genotipe, ditemukan SNP pada genotipe tertentu (SNP unik). Koleksi SNP dalam jumlah besar ini digunakan untuk mensintesis SNP chip untuk genotyping SDG secara cepat dan komprehensif. Didukung data fenotipe, SNP chip bermanfaat untuk melabel gen-gen unggul. Marka SNP yang berpautan dengan karakter unggul digunakan untuk menyeleksi individu pembawa karakter unggul tersebut. Dengan teknologi NGS, perakitan VUB tanaman dapat dilakukan lebih cepat, akurat, dan efisien. Dengan demikian, teknologi NGS dapat memfasilitasi karakterisasi dan pemanfaatan SDG untuk mem-percepat program pemuliaan tanaman.

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The complete mitochondrial genome of Xizicus (Haploxizicus) maculatus revealed by Next-Generation Sequencing and phylogenetic implication (Orthoptera, Meconematinae)

ZooKeys ◽

10.3897/zookeys.773.24156 ◽

2018 ◽

Vol 773 ◽

pp. 57-67 ◽

Cited By ~ 5

Author(s):

Mao Shaoli ◽

Yuan Hao ◽

Lu Chao ◽

Zhou Yafu ◽

Shi Fuming ◽

...

Keyword(s):

Next Generation Sequencing ◽

Mitochondrial Genome ◽

Base Composition ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Next Generation ◽

Protein Coding ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Xizicus Gorochov, 1993, the quiet-calling katydid, is a diverse genus with 68 species in world, which includes more than 45 species in China, has undergone numerous taxonomic revisions with contradicting conclusions. In this study the complete mitochondrial genome of Xizicus (Haploxizicus) maculatus collected from Hainan for the first time was sequenced using the Next-Generation Sequencing (NGS) technology. The length of whole mitogenome is 16,358 bp and contains the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition of the mitochondrial genome is 37.0 % A, 32.2 % T, 20.2 % C, and 10.6 % G. All 13 protein-coding genes (PCGs) began with typical ATN initiation codon. Nine of the 13 PCGs have a complete termination codon, but the remaining four genes (COI, COIII, ND5, and ND4) terminate with an incomplete T. Phylogenetic analyses are carried out based on the concatenated dataset of 13 PCGs and two rRNAs of Tettigoniidae species available in GenBank. Both Bayesian inference and Maximum Likelihood analyses recovered each subfamily as a monophyletic group. Regardless of the position of Lipotactinae, the relationships among the subfamilies of Tettigoniidae were as follows: ((((Tettigoniinae, Bradyporinae) Meconematinae) Conocephalinae) Hexacentrinae). The topological structure of the phylogeny trees showed that the Xizicus (Haploxizicus) maculatus is closer to Xizicus (Xizicus) fascipes than Xizicus (Eoxizicus) howardi.

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The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

10.1101/283788 ◽

2018 ◽

Author(s):

Maarten P.M. Vanhove ◽

Andrew G. Briscoe ◽

Michiel W.P. Jorissen ◽

D. Tim J. Littlewood ◽

Tine Huyse

Keyword(s):

Next Generation Sequencing ◽

Gene Order ◽

Stop Codon ◽

Start Codon ◽

Phylogenetic Position ◽

Next Generation ◽

Protein Coding ◽

Complete Mitogenome ◽

Generation Sequencing ◽

Mitochondrial Phylogeny

AbstractBackgroundMonogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to advance genetic work on African monogeneans by providing mitogenomic data of four species (two each belonging to the Gyrodactylidae and Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.ResultsBased on Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). The start codon TTG is new for Gyrodactylus and for the Dactylogyridae, as is the incomplete stop codon TA for the Dactylogyridae. The most variable markers are nad genes and these are under relaxed selection. Especially nad2 is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, rather than the supposedly ‘primitive’ African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.ConclusionsThe amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available while they constitute a risk to tropical aquaculture.

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