Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera (Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers

Wei, Zixiang; Chen, Fangjun; Ding, Hongxia; Liu, Wenli; Yang, Bo; Geng, Jiahui; Chen, Shihua; Guo, Shanli

doi:10.3390/genes14122183

Cited by 4 publications

(1 citation statement)

References 94 publications

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“…With the development of sequencing technology, more complete cp genomes have been reported. According to incomplete statistics, approximately 86 complete genomes of the Amaranthaceae family were deposited in the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/ (accessed on 22 April 2024) [27,[46][47][48][49][50]. However, merely one Krascheninnikovia species, K. ceratoides, was reported.…”

Section: Discussionmentioning

confidence: 99%

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis

Wei,

Li,

et al. 2024

Genes

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Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.

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Section: Discussionmentioning

confidence: 99%

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis

Wei,

Li,

et al. 2024

Genes

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Complete Plastid Genome Sequences of Four Salsoleae s.l. Species: Comparative and Phylogenetic Analyses

Almerekova,

Yermagambetova,

Osmonali

et al. 2024

Biomolecules

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The taxonomic classification of the genera Salsola L., Pyankovia Akhani and Roalson, and Xylosalsola Tzvelev within Chenopodiaceae Vent. (Amaranthaceae s.l.) remains controversial, with the precise number of species within these genera still unresolved. This study presents a comparative analysis of the complete plastid genomes of S. foliosa, S. tragus, P. affinis, and X. richteri species collected in Kazakhstan. The assembled plastid genomes varied in length, ranging from 151,177 bp to 152,969 bp for X. richteri and S. tragus. These genomes contained 133 genes, of which 114 were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Thirteen regions, including ndhC-ndhD, rps16-psbK, petD, rpoC2, ndhA, petB, clpP, atpF, ycf3, accD, ndhF-ndhG, matK, and rpl20-rpl22, exhibited relatively high levels of nucleotide variation. A total of 987 SSRs were detected across the four analyzed plastid genomes, primarily located in the intergenic spacer regions. Additionally, 254 repeats were identified, including 92 tandem repeats, 88 forward repeats, 100 palindromic repeats, and only one reverse repeat. A phylogenetic analysis revealed clear clustering into four clusters corresponding to the Salsoleae and Caroxyloneae tribe clades. These nucleotide sequences obtained in this study represent a valuable resource for future phylogenetic analyses within the Salsoleae s.l. tribe.

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Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae

He,

Liu,

Gao

et al. 2024

Horticulturae

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The Sapotaceae family comprises 65–70 genera and over 1250 species, holding significant ecological and economic value. Although previous studies have made some progress in the phylogenetic relationships and classification of Sapotaceae, many issues remain unresolved and require further in-depth research. In this study, we sequenced and assembled the complete chloroplast genomes of 21 plants from 11 genera of Sapotaceae, conducted a comparative genomic analysis, and performed a phylogenetic analysis by incorporating 16 previously published chloroplast genomes of Sapotaceae. The results showed that the chloroplast genome sizes in 21 plants of Sapotaceae range between 157,920 bp and 160,130 bp, exhibiting the typical quadripartite structure. Each genome contains 84–85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, while the ndhF gene is absent in Pouteria campechiana and Pouteria sapota. The relative synonymous codon usage (RSCU) analysis showed that isoleucine (Ile) is the most commonly used, while the codon for methionine (Met) is the least utilized. Additionally, five highly variable regions (petA-psbJ, psbI-trnS-GGA, rpl2_2-psbA, rps19-rpl2_2, and ycf4-cemA) and two coding sequences, ycf1 and matK, were identified as candidate molecular markers for species differentiation and a phylogenetic analysis within the Sapotaceae family. Phylogenetic trees were reconstructed using complete chloroplast genome sequences and analyzed using ML and BI methods, which revealed that the Sapotaceae family is divided into three distinct clades, each receiving strong statistical support (BS = 100, PP = 1). The intergeneric analysis revealed that Madhuca and Palaquium are sister groups (BS = 91, PP = 1), as are Gambeya and Chrysophyllum (BS = 91, PP = 1). Pouteria and Chrysophyllum are among the larger groups in the Sapotaceae family but the traditional classification boundaries of these genera are unstable and unfeasible, as the current genus boundaries fail to support their natural evolutionary relationships. In the phylogenetic tree, Eberhardtia aurata is placed on a separate branch. The morphological classification system shows that E. aurata has rust-colored pubescence on its branches, abaxial leaf surfaces, petioles, and other areas, which clearly distinguishes it from other genera. This study provides valuable insights into advancing phylogenetic research, population genetics, molecular breeding, and conservation strategies by comparing chloroplast genome structures and characteristics and constructing phylogenetic trees.

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Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera (Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers

Cited by 4 publications

References 94 publications

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis

Complete Plastid Genome Sequences of Four Salsoleae s.l. Species: Comparative and Phylogenetic Analyses

Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae

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