The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae)

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

doi:10.1080/23802359.2019.1598788

Cited by 13 publications

(9 citation statements)

References 11 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%

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%

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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“…These long gaps on the chloroplast genome are also found in Coffea arabica (Park et al, 2019e), Duchesnea chrysantha (Park et al, 2019c), and Illicium anisatum (Park et al, 2019d). This type of gap was also identified on the mitochondrial genomes of Liriodendron tulipifera (Park et al, 2019b) and Populus alba × glandulosa (Park et al, 2019f).…”

Section: Nucleotide Diversity Among Six Viburnum Speciesmentioning

confidence: 66%

Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea

Park¹,

Xi²,

2020

Korean J. Pl. Taxon

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Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

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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: 87%

“…In addition, A. thaliana and Arabidopsis suecica are clustered because the maternal origin of A. suecica is A. thaliana [ 101 ] ( Figure 7 ). Moreover, the topology of BI tree for the remaining Arabidopsis species, except for A. thaliana and A. suecica , is somewhat inconsistent to those of NJ and ML trees ( Figure 7 ), which has also been found in various plant chloroplast genomes [ 15 , 20 , 28 , 51 , 67 , 69 , 72 , 79 , 91 , 92 , 102 – 109 ]. This suggests that detailed investigations of phylogenetic relationships among Arabidopsis species with various methods should be done in near future.…”

Section: Resultsmentioning

confidence: 92%

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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The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae)

Cited by 13 publications

References 11 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

Comparative chloroplast genomics and phylogenetic analysis of the <i>Viburnum dilatatum</i> complex (Adoxaceae) in Korea

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

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