The complete chloroplast genome of <i>Leucobryum juniperoideum</i> (brid.) C. Müll. (Leucobryaceae, Bryophyta)

Min, Juhyeon; Kwon, Woochan; Xi, Hong; Park, Jongsun

doi:10.1080/23802359.2019.1661301

Cited by 7 publications

(5 citation statements)

References 17 publications

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“… 2020 ), L. juniperoideum (MK952779, Min et al. 2019 ), L. incana (NC_042174), M. maximowiczii (MT726030, Han et al. 2020b ), O. rogeri (NC_026212), P. patens (NC_005087), P. inflexum (MK131349), P. nutans (NC_045869, Jin et al.…”

Section: Resultsmentioning

confidence: 99%

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae)

Yuan,

Wang,

Sulayman

2024

Mitochondrial DNA Part B

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Whether Barbella flagellifera (Cardot) Nog. belongs to Neodicladiella has not yet been determined, and a study of the complete chloroplast (cp) genome of B. flagellifera would aid in determining its evolutionary position. In this study, we aimed to sequence the complete cp genome of B. flagellifera , an epiphytic species found in tropical and subtropical forests. The complete cp genome is 125,025 base pairs (bp) long and appears as a typical quadrilateral structure with a large single-copy (86,854 bp), a small single-copy (18,473 bp), and a pair of inverted repeats (19,698 bp). The overall GC content of the sequence is 41.0% and the genome encodes 127 genes, including 82 protein-coding genes, 37 tRNAs, and eight rRNAs. Phylogenetic analysis reveals that B. flagellifera clustered into a clade with other Hypnales groups with high bootstrap support. The complete cp genome presented here will provide helpful information for species identification of Barbella genus and Neodicladiella genus in Meteoriaceae.

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Section: Resultsmentioning

confidence: 99%

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae)

Yuan,

Wang,

Sulayman

2024

Mitochondrial DNA Part B

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“…NGS raw reads of truffle (SRA accession: SRR5005499) were downloaded from NCBI and processed under the Genome Information System (GeIS, http://geis.infoboss.co.kr) which has been utilized in various genomics studies. 7–9,13,14,17,19,20,25–83 SRR5005499 dataset used in this study contains 29,010,538 100-bp-reads (2,901,053,800 bp). In the pipeline, de novo assembly and confirmation were done by Velvet v1.2.10…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum

Park¹,

Lee²,

Park³

2022

Science Progress

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Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.

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“…After getting first draft of chloroplast genome sequences, gap was filled with GapCloser v1.12 (Zhao et al, 2011) and all bases from the assembled sequences were confirmed using BWA v0.7.17 (Li, 2013) and SAMtools v1.9 (Li et al, 2009). All bioinformatic processes for de novo assembly was conducted by the pipeline, Genome Information System (GeIS; http://geis.infoboss.co.kr), which has been efficiently utilized and optimized in the previous studies (Min et al, 2019;Yun et al, 2019;Kim et al, 2021aKim et al, , 2021bPark et al, 2021b).…”

Section: De Novo Assembly and Annotation Of Diarthron Linifolium Chloroplast Genomementioning

confidence: 99%

The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia

Park²

2021

Korean J. Pl. Taxon

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Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.

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The complete chloroplast genome of Leucobryum juniperoideum (brid.) C. Müll. (Leucobryaceae, Bryophyta)

Abstract: The complete chloroplast genome of Leucobryum juniperoideum (brid.) C. M€ ull.

Cited by 7 publications

References 17 publications

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae)

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae)

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum

The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia

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