The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae)

Moreira, Daniel A.; Furtado, Carolina; Parente, Thiago Estevam

doi:10.1016/j.gene.2015.08.059

Cited by 17 publications

(22 citation statements)

References 32 publications

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“…Apart from the two Loricariidae mitogenomes mentioned above, three other (from Hypoptopoma incognitum , Accession: KT033767, from Ancistrus spp ., Accession: KP960569, and from the endangered species Hypancistrus zebra, Accession: KX611143.1) have recently been published by our group (Moreira et al, 2016, 2015; Magalhães et al 2016). …”

Section: Resultsmentioning

confidence: 99%

“…Mitochondrial genome was assembled using the mitochondrial transcripts sequenced in the liver transcriptome, following an approach described elsewhere (Moreira et al, 2015). Briefly, mitochondrial transcripts were retrieved by running a BLASTN search against the mitogenome of the closest related species with a complete mitogenome available, Pterygoplichthys disjunctivus (NC_015747.1) (Nakatani et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

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The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

Parente

Moreira

Magalhães

et al. 2017

Marine Pollution Bulletin

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Pterygoplichthys is a genus of related suckermouth armoured catfish native to South America that has invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled. Among the identified defensome genes, cytochromes P450 (CYP) were the most abundant, followed by nuclear receptors (NR), sulfotransferases (SULT) and ATP binding cassette transporters (ABC). A novel expansion in the CYP2Y subfamily was identified, as well as an independent expansion of the CYP2AAs. Two expansions were also observed among SULT1. Thirty-two transcripts were classified into twelve subfamilies of NR, while 21 encoded ABC transporters. The diversity of defensome transcripts sequenced herein could contribute to this species resistance to organic xenobiotics.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

Parente

Moreira

Magalhães

et al. 2017

Marine Pollution Bulletin

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“…The traditional protocols to produce the mitochondrial genomes have relied on performing either standard/long PCR or cloning, followed by a series of Sanger sequencing (Moreira, Furtado & Parente, 2015; Gan, Schultz & Austin, 2014; Poulsen et al, 2013). The classic method is a time consuming and resource demanding task (Hahn, Bachmann & Chevreux, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…The fast recovery, assembly, and annotation of mitogenome from genomic sequencing have been applied in butterflies and moths (Cong & Grishin, 2016), crayfish (Gan, Schultz & Austin, 2014), monogenean ectoparasitic flat-worms (Hahn, Bachmann & Chevreux, 2013), giant intestinal fluke ( Fasciolopsis buski ; Biswal et al, 2013) and Ascidian species (Rubinstein et al, 2013). In addition, RNA-seq and ultraconserved elements (UCE) sequencing are also excellent source to assemble mitochondrial genomes (Machado, Lyra & Grant, 2015; Moreira, Furtado & Parente, 2015; Raposo do Amaral et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

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

Yuan

Xia

Zeng

2016

PeerJ

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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 chunganensis and Quasipaa 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 of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

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“…Cleaned reads from the three individual fish were used for the de novo assembly of transcriptomes using the default parameters of Trinity (v. 2.0.2) (Haas et al, 2013). Mitochondrial genomes were assembled using the mitochondrial transcripts from the liver transcriptome, following the approach described by Moreira et al (2015aMoreira et al ( , 2015b. Briefly, mitochondrial transcripts were retrieved running a BLASTN search against the mitogenome of the closest related species with a complete mitogenome available, Corydoras rabauti (GI: 29501080) (Saitoh et al, 2003).…”

Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

et al. 2016

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The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

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The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae)

Cited by 17 publications

References 32 publications

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

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

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

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