Complete chloroplast genome of <i>Tulipa buhseana</i> (Liliaceae)

Ju, Xiuting; Tang, Nan; Shi, Guomin; Ye, Rongchun; Hou, Zhiqiang

doi:10.1080/23802359.2020.1773331

Cited by 4 publications

(3 citation statements)

References 7 publications

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“…Analyzing the codon preference of chloroplast genomes of 64 species in the Amaryllidaceae family, it was found that the variation range of G + C content between chloroplast genomes of different species is 0.38-0.39, with GC content less than 0.5, indicating that the GC content in chloroplast genomes of Lycoriaceae plants is less than AT content; The frequency changes of thymine T3s, cytosine C3s, adenine A3s, and guanine G3s in the third position of the synonymous codon range from 0.39 to 0.42, 0.23 to 0.25, 0.24 to 0.42, and 0.22 to 0.24, respectively; The variation range of G + C content in the third position of synonymous codon is 0.34 ~ 0.37, and the GC3s content is less than 0.5, indicating that the chloroplast genome of plants in the Amaryllidaceae family prefers to use synonymous codons ending in A/U; The range of Nec is between 54.64 and 56.16, with a higher Nec value, indicating weak codon usage bias in the chloroplast genome of Amaryllidaceae plants; The range of CAI is between 0.154 and 0.162, with a relatively low CAI value. The CBI range is between − 0.102 and − 0.079, with an average value of -0.092, indicating that there is a certain degree of preference in the chloroplast genome codons of these 64 Amaryllidaceae plants, but the preference is weak [94][95][96][97][98] .…”

Section: Codon Preference Analysis Of Chloroplast Genome Inamaryllida...mentioning

confidence: 99%

Characteristics analysis of chloroplast genome and molecular evolution of chloroplast genes in Amaryllidaceae plants

Chen

2023

Preprint

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Background Amaryllidaceae is a family of Monocotyledons in Liliflorae, and is considered an important ornamental and economic plant due to its usually showy flowers, and the Amaryllidaceae also has enormous medicinal value. Currently, the gene structure characteristics and molecular function analysis of all chloroplast genomes in Amaryllidaceae are rarely reported, so this study mainly analyzed the gene structure characteristics and molecular function of all chloroplast genomes in Amaryllidaceae to reveal the characteristics of the chloroplast genome of Amaryllidaceae plants and explore their evolution and development patterns, and it used bioinformatics methods to analyze the chloroplast genome sequences of 64 Amaryllidaceae plants that have been published on NCBI. Results Among the 64 species of Amaryllidaceae plants, the species with a gene number of 86 had the most chloroplasts, with 38 species accounting for approximately 59%. The number of rRNAs in its chloroplast genome is all 8. There are 55 species of plants in the Amaryllidaceae with 38 tRNAs, and only a few species have abnormal tRNA numbers in their chloroplast genomes due to the loss or duplication of tRNA genes. The GC content of chloroplast genomes in all species ranges from 36–39%, indicating that their AT content is roughly between 61–64%. The high proportion of AT content in chloroplast genomes indicates that chloroplast codons prefer to use A/T bases. By constructing a phylogenetic evolution tree, it was found that the 64 species of Amaryllidaceae plants can be divided into 12 evolutionary groups. Lycoris longituba and Lycoris anhuiensis have the fastest evolutionary speed, while Allium przewalskianum and Allium polyrhizum CMS-S have the most primitive and slowest evolutionary speed. By analyzing the codon preference of chloroplast genomes, it was found that plants in the Amaryllidaceae prefer to use synonymous codons ending in A/U, and their chloroplast genome codon usage bias is weak. Conclusion Our results preliminarily explored the relationship between each species in Amaryllidaceae, and the characteristics of the entire chloroplast genome sequence of Amaryllidaceae were revealed, these results provide a certain theoretical basis for further research on the plants of the Amaryllidaceae family in the future.

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Section: Codon Preference Analysis Of Chloroplast Genome Inamaryllida...mentioning

confidence: 99%

Characteristics analysis of chloroplast genome and molecular evolution of chloroplast genes in Amaryllidaceae plants

Chen

2023

Preprint

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“… 2020 ; Ju, Tang, et al. 2020 ). In this study, we worked on T. sinkiangensis Z. M. Mao 1980 which is a endemic species in China.…”

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The complete chloroplast genome ofTulipa sinkiangensisZ. M. Mao (Liliaceae) with multi-flower

Xing

Zhang

et al. 2023

Mitochondrial DNA Part B

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Tulipa sinkiangensis Z. M. Mao 1980 is endemic to Xinjiang Province, China. In this study, we reported the complete chloroplast genome of T. sinkiangensis . The complete chloroplast genome of T. sinkiangensis comprises 151,929 bp and was divided into four typical regions: a large single-copy region of 82,062 bp, a pair of inverse repeats of 26,361 bp each, and a small single-copy region of 17,145 bp. A total of 136 genes were identified in this chloroplast, of which 87 were protein-coding, 38 were tRNA, eight were rRNA, and three were pseudogene. The results of this study will provide valuable information for understanding evolution and identification of different species belonging to genus Tulipa .

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“…CDS, rRNA, and tRNA genes were predicted by Prodigal2.6.3, Hmmer3.1b2, and Aragorn1.2.38, respectively (Ju et al. 2020 ).…”

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The complete chloroplast genome of Digitaria sanguinalis (Graminales: Gramineae)

Jin

Zhang

et al. 2022

Mitochondrial DNA Part B

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Digitaria sanguinalis (Linnaeus) Scopoli 1722 is an annual herbal plant that has important medicinal and ecological value. The chloroplast genome was 138,079 bp in length. In total, 129 genes were predicted, including 82 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall AT content of the genome was 61.39%. The phylogenetic analysis showed that D. sanguinalis and D . glauca formed a base clade in Panicoideae close to Thyridolepis xerophila . This study will help to understand the genetic diversity of the Digitaria plants.

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Complete chloroplast genome of Tulipa buhseana (Liliaceae)

Cited by 4 publications

References 7 publications

Characteristics analysis of chloroplast genome and molecular evolution of chloroplast genes in Amaryllidaceae plants

Characteristics analysis of chloroplast genome and molecular evolution of chloroplast genes in Amaryllidaceae plants

The complete chloroplast genome ofTulipa sinkiangensisZ. M. Mao (Liliaceae) with multi-flower

The complete chloroplast genome of Digitaria sanguinalis (Graminales: Gramineae)

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