Complete sequence of mitochondrial DNA of <i>Gracilaria edulis</i> (Rhodophyta)

Sedanza, Mary Grace; Meinita, Maria Dyah Nur; Tang, Xianming; Chen, Weizhou; Yin, Hongxin; Liu, Cui; Jin, Yishuai; Shan, Changliang; Li, Yue; Liu, Tao

doi:10.1080/23802359.2017.1422413

Cited by 4 publications

(4 citation statements)

References 6 publications

(5 reference statements)

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“…Alternatively, the SNVs and ambiguities observed could be due to each dataset having been sequenced from DNA originating from multiple specimens. While mtDNA is typically sequenced from an individual specimen (see, for example, Lee et al, 2006;Zhao et al, 2011;Sedanza et al, 2020), the general procedure for the extraction of baculovirus occlusion bodies (OBs) is from multiple infected insects pooled together to increase the resulting yield. With the NGS data utilized in this study originally generated to determine the genome sequence of the baculovirus CrleGV, DNA was extracted from multiple T. leucotreta larvae, and therefore contains mtDNA from multiple specimens.…”

Section: Discussionmentioning

confidence: 99%

Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

Jukes

2021

Insect Molecular Biology

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Thaumatotibia leucotreta (Lepidoptera, Tortricidae) is one of many economically important insect pests for which no complete mitogenome sequence is available. The complete mitochondrial sequences for this species and other key pests could assist in the development of novel molecular techniques, such as enabling the identification of population-specific markers which could assist in improved monitoring of populations. The objective of this study was to determine whether NGS datasets generated for entomopathogenic viruses contain reads originating from host mitochondrial DNA. A total of 28 NGS datasets generated for the baculovirus Cryptophlebia leucotreta granulovirus (CrleGV) were analysed in this study. Three datasets contained sufficient reads providing adequate coverage for the assembly of complete mitogenomes. All 13 protein-coding genes, 22 tRNAs and both rRNAs present in the mitogenomes of other species within the Grapholitini tribe, were identified. Phylogenetic analysis of the mitogenomes at both an intrafamilial and interspecies level grouped the sequences within the Olethreutinae and T. leucotreta clades, respectively. Analysis of single nucleotide variations (SNVs) between each T. leucotreta sequence indicated up to 75 differences across the mitogenome. The methodology used in this study could be expanded to other baculovirus NGS datasets enabling the generation of novel lepidopteran mitogenome sequences.

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Section: Discussionmentioning

confidence: 99%

Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

Jukes

2021

Insect Molecular Biology

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“…Mitogenomes sequence is one of the fundamental approaches used to analyze the taxonomy and phylogeny of red algae (Boo et al 2016). Sedanza et al (2020) determined that the complete G. edulis mitogenome length was 25,708 bp and this species clustered together with G. changii and G. salicornia. Wang et al (2020) found G. chilensis plastid genome sequence was 185,640 bp and it had a closer relationship with Gracilaria tenuistipitata var.…”

Section: Molecular Identificationmentioning

confidence: 99%

“…Therefore, it is necessary because of being capable to provide more accurate information on a species genetic diversity. Some molecular studies of Gracilariaceae have been conducted (Liu et al 2017;Sedanza et al 2020;Wang et al 2020), but not in Indonesia. A molecular study of this country's Gracilaria species was conducted using RAPD marker (Windarsih et al 2019) to characterize their genetic profile with random single oligonucleotides, however, the RAPD also has limitations due to its low reproducibility.…”

Section: Introductionmentioning

confidence: 99%

Molecular identification of Gracilaria species (Gracilariales, Rhodophyta) obtained from the South Coast of Java Island, Indonesia

et al. 2021

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Abstract. Meinita MDN, Akromah N, Andriyani N, Setijanto, Harwanto D, Liu T. 2021. Molecular identification of Gracilaria species (Gracilariales, Rhodophyta) obtained from the South Coast of Java Island, Indonesia. Biodiversitas 22: 3046-3056. The study of seaweeds diversity and species identification is an important component of marine resource management. However, seaweed identification based on morphological characteristics has several limitations. Besides, DNA barcodes or the partial sequences of cytochrome c oxidase I (COX1) have been proved to identify seaweeds at the species level. To date, Gracilaria species molecular diversity has not been studied in the South Coast of Java Island. Hence, this study aimed to identify the Gracilaria spp. obtained from 6 different beaches along the South Coast of Java, based on the COX1 gene. COX1 gene utilization for identifying and observing the genetic diversity, both intraspecific (genetic variation within species) and interspecific (variations between species) of Gracilaria species in this study has produced good results. A total of 13 seaweed samples collected from beaches in this study were identified as Gracilaria salicornia, G. edulis, G. firma, and G. textorii. The results of genetic diversity analysis conducted using the COX1 gene showed the intraspecific diversity of G. edulis obtained from the beaches of Kondang Merak, Kukup, Nusakambangan, and Karapyak was included in the moderate diversity category. Also, the intraspecific diversity of G. salicornia obtained from the beaches of Kondang Merak, Kukup, and Nusakambangan was included in the moderate diversity category, while the intraspecific diversity of G. textorii from Menganti and Karapyak Beach had no diversity.

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“…Chloroplast genome of U. prolifera was taken as seed sequences for sequence splicing about the complete chloroplast genome of U. torta using NOVOPlasty software (Sedanza et al. 2020 ). The extended chloroplast genome contigs was obtained, and then the extended contigs were compared with the chloroplast genome sequence of U. prolifera to obtain the correct contig sequence.…”

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confidence: 99%

Characterization of complete chloroplast genome of Ulva torta (Mertens) Trevisan, 1841

Wen

Yang

et al. 2022

Mitochondrial DNA Part B

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Ulva torta (Mertens) Trevisan, 1841 was a global temperate widespread species. Green tide blooms caused by the green algae of the Ulva species occurred frequently in China. As a newly discovered species in the green tide bloom area, it was necessary to explore the relationship between U. torta and other green algae of the Ulva species. The complete chloroplast genome of U. torta was 105,423 bp in size. A total of 100 genes were annotated in the genome, containing 70 protein-coding genes, 27 transfer RNA (tRNA) genes, and three rRNA genes. The chloroplast genome had high AT content (74.76%). Phylogenetic analysis showed U. torta was clustered with Ulva meridionalis . This work could be useful for studying the evolution and genetic diversity of U. torta .

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Complete sequence of mitochondrial DNA of Gracilaria edulis (Rhodophyta)

Cited by 4 publications

References 6 publications

Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

Molecular identification of Gracilaria species (Gracilariales, Rhodophyta) obtained from the South Coast of Java Island, Indonesia

Characterization of complete chloroplast genome of Ulva torta (Mertens) Trevisan, 1841

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