The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation  of the Zoysia species

Oh, Sung‐Dug; Lee, Seong Kon; Yun, Doh-Won; Sun, Hui; Kang, Hong‐Gyu; Lee, Hyo-Yeon; Xi, Hong; Park, Jongsun; Lee, Bumkyu

doi:10.11110/kjpt.2021.51.3.326

Cited by 6 publications

(4 citation statements)

References 40 publications

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“…The retained nucleotides of ycf 2 varied from 105 to 792 bp for the 16 Aristidoideae species. The loss of ycf 1 and ycf 2 is similar to previously reported chloroplast genomes of Poaceae [ 30 , 56 , 57 ]. The genes ycf 1/2 have a higher degree of variation than the commonly used molecular maker mat K and are suitable for phylogenetic research [ 58 ].…”

Section: Discussionsupporting

confidence: 88%

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Guo

Zhang

et al. 2022

Biology

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Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.

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Section: Discussionsupporting

confidence: 88%

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Guo

Zhang

et al. 2022

Biology

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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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“…It is regarded as an invasive species in Korea and the elucidation of its genetic background will help identify it. This strategy was previously applied to Linepithema humile (Oh et al 2021; Park et al 2021a). Complete mitochondrial genomes have been utilized in an integrated system monitoring invasive pest insect species in Korea (Park et al 2020a).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the complete mitochondrial genome ofMelanoplus differentialis(Acrididae: Melanoplinae) captured in Korea

Kim

Lee

et al. 2023

Entomological Research

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In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species‐level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies.

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The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Cited by 6 publications

References 40 publications

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

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

Comprehensive analysis of the complete mitochondrial genome ofMelanoplus differentialis(Acrididae: Melanoplinae) captured in Korea

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