Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Nie, Xiaojun; Zhao, Xian; Wang, Sue; Zhang, Ting; Li, Chong; Liu, Hui; Tong, Wei; Guo, Yuan

doi:10.3390/agronomy8090159

Cited by 19 publications

(6 citation statements)

References 54 publications

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“…In the IR of T. sinskajae the GC-content reaches 43.9%. The higher content of GC pairs in the IR zone can be explained by the presence of 4 rRNA genes in this region, which is consistent with the results of analysis of chloroplast DNA of other plants (Bosacchi et al 2015;Nie et al 2018).…”

Section: Phylogenetic Analysissupporting

confidence: 90%

Sequencing and analysis of complete plastid genomes of diploid wheats Tritcum sinskajae and Triticum monococcum k-20970

Azat,

Bulat,

Alexey

2023

Preprint

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Diploid wheat with genome A Triticum sinskajae A. Filat. et Kurk. was discovered in the early 70s. last century during the reproduction of samples of Triticum monococcum L. line k-20970. Despite the fact that T. sinskajae was initially proposed to be identified as a separate wheat species, in further studies it was considered as a spontaneous mutant of T. monococcum. A number of studies have shown that T. sinskajae is genetically different from different T. monococcum lineages, but how different it is from the T. monococcum k-20970 lineage remained unknown. Based on this, the purpose of this study was to sequence and compare the chloroplast genomes of T. sinskajae and T. monococcum line k-20970, as well as to clarify the phylogenetic relationships between diploid wheats based on the results of analysis of the nucleotide sequences of their chloroplast genomes. During this study, we were the first to sequence and annotate the complete chloroplast genomes of T. sinskajae k-48993 (Dagestan), T. monococcum k-20970 (Turkey), T. boeoticum k-58674 (Armenia) on a Genolab M sequencer (GeneMind, China). For comparative analysis, chloroplast genome sequences of T. monococcum subsp. monococcum (LC005977.1) and T. urartu (KJ614411.1) were taken from GenBank. According to the results of the analysis, it turned out that T. sinskajae (k-48993) and T. monococcum k-20970, although they were closer to each other, differed in 10 changes in the chloroplast genome, including 3 substitutions, 1 transversion, 1 deletion, 4 insertions and 4bp inversion of AGAA with TTCT in the rbcL-psal intergenic region. The identified differences in the chloroplast genomes of T. sinskajae (k-48993) and T. monococcum (k-20970) allow us to conclude that they are two very close, but still different species of diploid wheat. A comparison of the chloroplast genomes of diploid wheats showed a common origin of the plasmons of three closely related einkorns - T. sinskajae, T. monococcum and T. boeoticum, while T. urartu is located a little further from them.

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Section: Phylogenetic Analysissupporting

confidence: 90%

Sequencing and analysis of complete plastid genomes of diploid wheats Tritcum sinskajae and Triticum monococcum k-20970

Azat,

Bulat,

Alexey

2023

Preprint

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“…All the predicted RNA editing sites resulted in the conversion of cytosine to uracil predominantly at the 2nd position of the codon. The predominant RNA editing type revealed in the A. littoralis cp genome was comparable to that observed in rice 51 , proso millet 52 , wheat 53 , and maize 33 . Intriguingly, cytosine—uracil conversion is the most common RNA editing type in plants 54 .…”

Section: Discussionsupporting

confidence: 54%

The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species

Ben Romdhane,

Al-Doss,

Hassairi

2024

Sci Rep

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Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.

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“…With the development of next-generation sequencing technologies, provides a cost-effective means and efficiently get complete chloroplast genome information, which can contribute to the resolution of species relationships. Moreover, the comparative analysis of chloroplast genomes can contribute to a theoretical basis for a phylogenetic status study [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

Zhang

Rong

et al. 2018

Molecules

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Malus hupehensis belongs to the Malus genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of Malus hupehensis, using a Hiseq X Ten sequencing platform, is reported. The M. hupehensis cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine Malus complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that M. hupehensis clustered closer ties with M. baccata, M. micromalus, and M. prunifolia than with M. tschonoskii. The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the Malus and related species.

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Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Cited by 19 publications

References 54 publications

Sequencing and analysis of complete plastid genomes of diploid wheats Tritcum sinskajae and Triticum monococcum k-20970

Sequencing and analysis of complete plastid genomes of diploid wheats Tritcum sinskajae and Triticum monococcum k-20970

The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species

Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

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