The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania

Sun, Liyong; Jiang, Zheng; Wan, Xiaoxia; Zou, Xuan; Yao, Xin; Wang, Yaling; Yin, Zengfang

doi:10.1016/j.gene.2020.144410

Cited by 20 publications

(18 citation statements)

References 47 publications

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“…The most abundant SSR motif was mononucleotide repeats followed by trinucleotide and tetranucleotide repeats in detected SSRs. This result is not completely consistent with other ndings that showed mono-and di-nucleotides are the most frequent SSR types in plant cp genomes [41][42][43], but is consistent with the report in Lythraceae [44] and Magnolia polytepala [12], and is also in accord with the nding of SSR mining from the E. ophiuroides RNA-seq data although mononucleotide repeat was omitted in that study [45]. Whether mononucleotide SSRs or polynucleotide SSRs detected in the present study, most of them were rich in A/T content.…”

Section: Repeat Sequencesupporting

confidence: 65%

“…Therefore, cp genome sequence data can provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals [9,10], which could contribute greatly to plant breeding and conservation strategies. In addition, cp DNA has the characteristics of non-recombinant nature, low mutation rates, and uniparental inheritance, which makes it signi cant in giving insights into plant evolution and developing applications for biotechnological breeding [11,12]. In recent years, with the rapid development of nextgeneration sequencing (NGS) technology, it is now more convenient and relatively inexpensive to obtain cp genome sequences and implement whole genome-based phylogenomics [13].…”

Section: Introductionmentioning

confidence: 99%

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Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Zong

Wang

et al. 2021

Preprint

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Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

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Section: Repeat Sequencesupporting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Zong

Wang

et al. 2021

Preprint

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“…Among them, leucine (Leu) is used the most, and cysteine (Cys) is used the least. Such bias is considered to be a comprehensive result of natural selection, species mutation, and genetic drift [ 29 , 30 ]. The complete chloroplast genome with gene annotations has been uploaded to the NCBI database, the accession numbers of D. tanguticum and D. moldavica are MT457746 and MT457747, respectively.…”

Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

Yao

Zhao

et al. 2020

BioMed Research International

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Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene’s lengths of 82,221 bp and 81,450 bp, large single-copy region’s (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region’s (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region’s (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.

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“…The chloroplast genome sequence of Atractylodes japonica was 153,208 bp in length and showed a conserved quadripartite structure like most angiosperm plants such as Withania somnifera (Mehmood et al 2020) and Magnolia polytepala (Sun et al 2020), with two reverse repeated regions (IRa and IRb) of 25,147 bp in length. The repeat regions divided the entire genome into two single-copy regions, namely a small single-copy region (SSC) and a large single-copy region (LSC) with 18,659 bp and 84,255 bp, respectively.…”

mentioning

confidence: 99%

“… 2020 ) and Magnolia polytepala (Sun et al. 2020 ), with two reverse repeated regions (IRa and IRb) of 25,147 bp in length. The repeat regions divided the entire genome into two single-copy regions, namely a small single-copy region (SSC) and a large single-copy region (LSC) with 18,659 bp and 84,255 bp, respectively.…”

mentioning

confidence: 99%

The complete chloroplast genome of Atractylodes japonica Koidz. ex Kitam. and its phylogenetic inference

Shi

Xie

Zhao

et al. 2021

Mitochondrial DNA Part B

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Atractylodes japonica Koidz. ex Kitam. is a perennial herbal plant, and its dried rhizomes have been widely used as traditional medicine in China and Japan. In this study, we assembled and annotated the complete chloroplast (cp) genome sequence of A. japonica using the high-throughput sequencing approach. The cp genome of A. japonica is 153,208 bp in length with the overall GC content of 37.7%, including two inverted repeat (IR) regions of 25,147 bp, which was separated by a large single-copy (LSC) region of 84,255 bp and a small single-copy (SSC) region of 18,659 bp. 113 unique genes were annotated in the genome, including 80 protein-coding genes, 29 represented tRNA genes, and four denoted rRNA genes. A maximum-likelihood phylogenetic analysis with 38 complete cp sequences showed that Atractylodes formed a monophyletic clade, and A. japonica and A. koreana formed a subclade in Atractylodes. This study provides the chloroplast genome structure features and phylogenetic relationship of A. japonica.

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The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania

Cited by 20 publications

References 47 publications

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

The complete chloroplast genome of Atractylodes japonica Koidz. ex Kitam. and its phylogenetic inference

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