Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes

Hupfer, H.; Świątek, M.; Hornung, Severin; Herrmann, Reinhold G.; Maier, Rainer M.; Chiu, Wan-Ling; Sears, Barbara B.

doi:10.1007/pl00008686

Cited by 75 publications

(9 citation statements)

References 30 publications

(16 reference statements)

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“…Large inversions are well characterized in the chloroplast genomes of various plant families/genera and the sequence data have been used to determine angiosperm lineages from the genus to phylum level (Jansen and Palmer, 1987; Milligan et al, 1989; Raubeson and Jansen, 1992; Hupfer et al, 2000; Kim and Lee, 2005). In contrast, limited plant groups were studied involving small inversions.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

Dong

Li³

et al. 2017

Front. Plant Sci.

115

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Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in Juglans. Classification of Juglans at section level is problematic, because the phylogenetic position of Juglans cinerea is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of Juglans were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus. The Juglans chloroplast genomes possessed the typical quadripartite structure of angiosperms, consisting of a pair of inverted repeat regions separated by a large single-copy region and a small single-copy region. All the 10 chloroplast genomes possessed 112 unique genes arranged in the same order, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A combined sequence data set from two nuclear DNA regions revealed that Juglans plants could be classified into three branches: (1) section Juglans, (2) section Cardiocaryon including J. cinerea which is closer to J. mandshurica, and (3) section Rhysocaryon. However, three branches with a different phylogenetic topology were recognized in Juglans using the complete chloroplast genome sequences: (1) section Juglans, (2) section Cardiocaryon, and (3) section Rhysocaryon plus J. cinerea. The molecular taxonomy of Juglans is almost compatible to the morphological taxonomy except J. cinerea (section Trachycaryon). Based on the complete chloroplast genome sequence data, the divergence time between section Juglans and section Cardiocaryon was 44.77 Mya, while section Rhysocaryon diverged from other sections in the genus Juglans was 47.61 Mya. Eleven of the 12 small inversions in the chloroplast genomes provided valuable phylogenetic information for classification of walnut plants at section and species levels. Our results are valuable for future studies on Juglans genetic diversity and will enhance the understanding on the phylogenetic evolution of Juglandaceae.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

Dong

Li³

et al. 2017

Front. Plant Sci.

115

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“…Studies have shown that plastomes in many angiosperm lineages have genomic structural differences, called inversions, ranging from small to large inversions, which provide important phylogenetic information ( Figure 2 ). These include Onagraceae ( Hupfer et al., 2000 ), Asteraceae ( Walker et al., 2014 ), Fabaceae ( Wang et al., 2018 ; Charboneau et al., 2021 ), and Commelineaceae ( Jung et al., 2021 ). Previously, Jung et al.…”

Section: Discussionmentioning

confidence: 99%

A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences

2023

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The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies—Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae—which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies—Crocoideae, Nivenioideae, and Aristeoideae—shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.

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“…Unlike the genomes of typical angiosperms [21][22][23][24], those of Zoysia lack the genes accD, ycf1, and ycf2 and introns in the clpP and rpoC1 genes, which is a pattern observed in most grasses [25][26][27]. The loss of two introns in the clpP gene has been reported independently in different angiosperm families, including Poaceae [28][29][30], the IR-lacking clade of Leguminosae [31], Oleaceae (opposite-leaved Jasminum and Menodora) [32], and Onagraceae (Oenothera) [33].…”

Section: Discussionmentioning

confidence: 99%

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Cheon

Woo

et al. 2021

Plants

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The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

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Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes

Cited by 75 publications

References 30 publications

Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

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