Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species

Luo, Chen; Yang, Li; Budhathoki, Roshani; Shi, Jiyuan; Yer, Huseyin; Yan, Bo; Wang, Qiong; Wen, Yonghui; Huang, Meijuan; Huang, Haiquan

doi:10.1371/journal.pone.0248182

Cited by 8 publications

(3 citation statements)

References 48 publications

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“…Occasional short sequence repeats and mutations in DNA sequences can be extended into longer tandem repeats through slip-chain mismatch events, and transposon-mediated insertion and copy slip may be responsible for both direct and reverse dispersed repeats (Levinson and Gutman, 1987). In this paper, the forward and palindromic repeats were the most common repeat types and most of the dispersed repeats were less than 40 bp, as the previous studies was reported (Liu et al, 2019;Kirov et al, 2020;Luo et al, 2021).…”

Section: Discussionmentioning

confidence: 50%

Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

et al. 2022

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Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.

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Section: Discussionmentioning

confidence: 50%

Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

et al. 2022

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“…The reference I. tectorum genome (153,253 bp) was the third in size. The coding regions had less divergence than the noncoding sequence regions owing to the variable regions [92][93][94]. The IR regions were more conserved, whereas the LSC and SSC regions were more divergent.…”

Section: Identification Of Highly Variablementioning

confidence: 99%

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Feng

Wang

et al. 2022

BioMed Research International

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Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.

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“…The chloroplast genome (CpDNA) and nuclear genome were currently widely used in plant genetic diversity, phylogenetic relationships, and lineage geography. Luo et al (2021a, b) sequenced the chloroplast genome of some Impatiens and identi ed some long repeat sequences and simple repeats, which provided valuable and important genomes for Impatiens species identi cation and phylogenetic evolution. Our research aimed to systematically investigate Impatiens in eastern Yunnan, and provide basic data for the protection of Impatiens resources and species diversity in this area.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Analysis of Impatiens in the Eastern Yunnan, China

Zhao

Yang

et al. 2023

Preprint

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Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. In this study, ISSR, trnL-trnnF, atpB-rbcL and DEF four molecular markers were used to analyze the genetic diversity and phylogenetic relationships among 32 species of Impatiens from eastern Yunnan. The results showed that the genetic similarity coefficient (GS) of these Impatiens resources ranged from 0.540 to 0.990, it indicated that the genetic diversity was relatively rich. However the genetic distance was relatively vague, and the evolutionary relationship was not obvious, which the phylogenetic trees were constructed by using the chloroplast genes atpB-rbcL and trnL-trnF. The genetic distance of the phylogenetic tree constructed by the DEF gene was relatively clear, the evolutionary relationship was obvious, and the result was consistent with ISSR. This indicated that DEF gene was greatly affected by plant habitat, and had abundant variation and a fast evolution rate, while atpB-rbcL and trnL-trnF genes had a slower evolution rate. And it was discovered that the flower morphological traits of the genus Impatiens can be employed as significant categorization markers. In particular, the wing shape can be used as an important flower morphological feature for the classification of the genus Impatiens in eastern Yunnan; and the results of using ISSR and DEF gene markers and flower morphological characteristics were consistent with the results of the interspecies division of Impatiens in this region. This study provided new basic data and a scientific basis for the protection, sustainable development, and utilization of Impatiens plant resources and genetic breeding in this region.

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Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species

Cited by 8 publications

References 48 publications

Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Phylogenetic Analysis of Impatiens in the Eastern Yunnan, China

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