The complete chloroplast genome of tulip tree, <i>Liriodendron tulifipera</i> L. (Magnoliaceae): investigation of intra-species chloroplast variations

Park, Jongsun; Kim, Yongsung; Kwon, Woochan; Xi, Hong; Kwon, Mi

doi:10.1080/23802359.2019.1598822

Cited by 10 publications

(6 citation statements)

References 23 publications

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“…This result suggests that next-generation sequencing technology that provides a large number of short reads can be used to provide evidence for the existence of endosymbiont species using DNA extracted from insect species. These results draw comparison to previous studies that have successfully identified a multiple number of complete organelle or bacterial genomes from one NGS library [12,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37].…”

Section: Introductionsupporting

confidence: 65%

“…This suggests that these insect-hosted fungal endosymbionts have been evolved independently from the other fungal species in the Ophiocordycipitaceae family. Owing to the advantages of NGS raw reads, which can detect sequences from unknown or unexpected organisms [12,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37], we successfully identified the complete mitogenomes of WBPH fungal endosymbionts within the NGS raw reads, suggesting that we can understand their phylogenetic positions of fungal symbiont with high resolution without the need to isolate the symbiont from the host. Furthermore, our study shows that NGS raw reads of insects generated in the future can be used to pinpoint further fungal endosymbionts that have previously been difficult to identify.…”

Section: Discussionmentioning

confidence: 99%

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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

Choi

Xi²,

Park³

2021

International Journal of Genomics

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Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.

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Section: Introductionsupporting

confidence: 65%

Section: Discussionmentioning

confidence: 99%

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

Choi

Xi²,

Park³

2021

International Journal of Genomics

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“…It is caused by 6 bp deletion on ycf2 located in the IR region compared to the rest five A. thaliana chloroplast genomes. Interestingly, Tsu0 shows the longest length of chloroplast genome, caused by an insertion of approximately 500 bp between trnL and trnF , which is similar to the cases of Coffea arabica with one continuous insertion region [ 50 ], Duchesnea chrysantha showing three continuous insertion regions [ 21 ], Viburnum amplificatum showing two continuous insertion regions [ 32 ], and mitochondrial genomes of Populus tremula x Populus glandulosa and Liriodendron tulipifera with four and thirty-three continuous insertion regions, respectively [ 51 , 52 ].…”

Section: Resultsmentioning

confidence: 82%

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

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“…Considering the other members of the Magnoliid clade, Persea was found to have 81 protein-coding genes, whereas Cinnamomum and Calycanthus of Laurales ( Chen et al., 2018 ) and Liriodendron of Magnoliales ( Park et al., 2019 ) consist of 84 protein-coding genes. Cinnamomum and Persea comprise 36 tRNA, whereas Calycanthus and Liriodendron have 37 tRNAs.…”

Section: Resultsmentioning

confidence: 99%

The chloroplast genome of black pepper (Piper nigrum L.) and its comparative analysis with related Piper species

et al. 2023

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Piper nigrum, also known as black pepper, is an economically and ecologically important crop of the genus Piper. It has been titled as the king of spices due to its wide consumption throughout the world. In the present investigation, the chloroplast genome of P. nigrum has been assembled from a whole genome sequence by integrating the short and long reads generated through Illumina and PacBio platforms, respectively. The chloroplast genome was observed to be 161,522 bp in size, having a quadripartite structure with a large single copy (LSC) region of 89,153 bp and a small single copy (SSC) region of 18,255 bp separated by a copy of inverted repeats (IRs), each 27,057 bp in length. Taking into consideration all the duplicated genes, a total of 131 genes were observed, which included 81 protein-coding genes, 37 tRNAs, 4 rRNAs, and 1 pseudogene. Individually, the LSC region consisted of 83 genes, the SSC region had 13 genes, and 18 genes were present in each IR region. Additionally, 216 SSRs were detected and 11 of these were validated through amplification in 12 species of Piper. The features of the chloroplast genome have been compared with those of the genus Piper. Our results provide useful insights into evolutionary and molecular studies of black pepper which will contribute to its further genetic improvement and breeding.

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The complete chloroplast genome of tulip tree, Liriodendron tulifipera L. (Magnoliaceae): investigation of intra-species chloroplast variations

Abstract: View related articles View Crossmark data Citing articles: 2 View citing articles MITOGENOME ANNOUNCEMENT The complete chloroplast genome of tulip tree, Liriodendron tulifipera L. (Magnoliaceae): investigation of intra-species chloroplast variations

Cited by 10 publications

References 23 publications

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

The chloroplast genome of black pepper (Piper nigrum L.) and its comparative analysis with related Piper species

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