Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Zhu, Min; Feng, Peipei; Ping, Jingyao; Li, Jinye; Su, Yingjuan; Wang, Ting

doi:10.1002/ece3.8151

Cited by 19 publications

(18 citation statements)

References 54 publications

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“…Previously, we noted that distribution characteristics of cp SSRs may provide useful phylogenic information at the genus level [ 48 ]. Here, we further evaluated the phylogenetic significance of mt SSRs based on the mt tree ( Figure 6 ).…”

Section: Resultsmentioning

confidence: 99%

“…Additionally, we also identified a total of 20 mtSSRs in O. vulgatum with sizes ranging from 10 to 48 bp. Previously, the distribution characteristics of cp SSRs were found to be capable of providing phylogenetic signals at the genus level [ 48 ]. In this study, similar characteristics were indeed observed in the mtSSRs of O. vulgatum and O. californium .…”

Section: Discussionmentioning

confidence: 99%

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The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

Hao

Liang

et al. 2022

Genes

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Many plant mitochondrial (mt) genomes have been sequenced but few in ferns. Ophioglossum vulgatum represents a typical species of fern genus Ophioglossum with medicinal and scientific value. However, its mt genome structure remains to be characterized. This study assembled and annotated the complete O. vulgatum mt genome and presented its structural characters and repeat sequences firstly. Its mt and chloroplast (cp) transfer sequences were explored, and the phylogenetic significance of both mt and cp genomes was also evaluated at the family level. Our results showed that the complete mt genome of O. vulgatum is a single circular genome of 369,673 bp in length, containing 5000 dispersed repetitive sequences. Phylogenetic trees reconstructed from cp and mt genomes displayed similar topologies, but also showed subtle differences at certain nodes. There exist 4818 bp common gene fragments between cp and mt genomes, of which more than 70% are located in tRNA intergenic regions (in mt). In conclusion, we assembled the complete mt genome of O. vulgatum, identified its remarkable structural characters, and provided new insights on ferns. The complementary results derived from mt and cp phylogeny highlighted that some higher taxonomic-level phylogenetic relationships among ferns remain to be resolved.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

Hao

Liang

et al. 2022

Genes

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“…Genetic variations in G. mangostana cultivars have been shown by randomly amplified DNA fingerprinting (RAF) and inter simple sequence repeat (ISSR) molecular markers 55–57 . Plastomes also contain SSR and long repeats 58,59 . SSR, which is a stretch of 1-6 bp small repeats, is found extensively in different regions of plastome such as the intergenic regions, intron regions, and protein-coding regions 23 .…”

Section: Discussionmentioning

confidence: 99%

“…Plastomes also contain SSR and long repeats 58,59 . SSR, which is a stretch of 1-6 bp small repeats, is found extensively in different regions of plastome such as the intergenic regions, intron regions, and protein-coding regions 23 .…”

Section: Genetic Variations In G Mangostana Cultivars Have Been Shown...mentioning

confidence: 99%

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Wee

Muhammad

Subbiah

et al. 2022

Preprint

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The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

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“…In previous study, however, the distribution of SSRs was reported to be lineage-speci c. Ping, Feng, Hao et al (2021) found the distributions of SSRs in Cupressus and Hesperocyparis were highly uniform, and suggested that Callitropsis funebris was closer to Cupressus than other Callitropsis species. Recently, Zhu et al (2021) found that the number, type, and localization of SSRs in the plastomes of Cyatheaceae were inter-genus speci c, which provide valid evidence for the phylogenetic analysis of Cyatheaceae.…”

Section: Diversity Of Ssrs Distribution Patternsmentioning

confidence: 95%

Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content

Gan

Liu

Ping

et al. 2022

Preprint

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In recent years, the evolution and phylogeny of plastid genomes have attracted much attention from scholars all over the world. Annonaceae is the largest family in Magnoliales with the greatest diversity among and within genera. Thus comparative analyses of its plastomes will be informative. In this study, the complete chloroplast genome of Miliusa glochidioides was sequenced by next-generation sequencing technology. Using two Magnoliaceae species as out-group, a comparative analysis of the existing 13 Annonaceae plastomes was conducted, and a phylogenetic relationship was constructed based on four methods. Our results show that the Annonaceae plastomes have great variation in the evolution process. The genome size is between 159kb and 202kb while the gene content ranges from 127 to 165. The number of genes in the IR region is between 5 and 39. Plastomes underwent significant structural rearrangements, including one inversion and multiple large-scale expansion (6-20kb) in the lR region, and shrinkage and inversions in the SSC region. Compared with Magnoliaceae, two fragments (pafII-atpE and 5'-rps12-psbJ) were inversed in Annonaceae. The phylogenetic relationship based on 78 common protein genes showed that Cananga odorata was located at the base of Annonaceae. Annonoideae was a monophyletic group, and Chieniodendron hainanense was located inside the Malmeoideae. A total of 737 simple sequence repeats (SSRs) were detected in the study, and the distribution of SSRs varied from species. It is mainly dominated by A/T bases (mononucleotide) and is located in the intergenic region. In conclusion, the plastomes of Annonaceae have undergone great variation during evolution, especially the large-scale expansion of the IR region. Our study provides more information for studying the plastome evolution of Annonaceae.

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Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Cited by 19 publications

References 54 publications

The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content

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