86 research outputs found

    PCR amplified <i>ndh</i> genes among 23 <i>Cymbidium</i> species including hybrids and three closely related taxa.

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    <p>PCR amplified <i>ndh</i> genes among 23 <i>Cymbidium</i> species including hybrids and three closely related taxa.</p

    Independent degradation in genes of the plastid <i>ndh</i> gene family in species of the orchid genus <i>Cymbidium</i> (Orchidaceae; Epidendroideae)

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    <div><p>In this paper, we compare <i>ndh</i> genes in the plastid genome of many <i>Cymbidium</i> species and three closely related taxa in Orchidaceae looking for evidence of <i>ndh</i> gene degradation. Among the 11 <i>ndh</i> genes, there were frequently large deletions in directly repeated or AT-rich regions. Variation in these degraded <i>ndh</i> genes occurs between individual plants, apparently at population levels in these <i>Cymbidium</i> species. It is likely that <i>ndh</i> gene transfers from the plastome to mitochondrial genome (chondriome) occurred independently in Orchidaceae and that <i>ndh</i> genes in the chondriome were also relatively recently transferred between distantly related species in Orchidaceae. Four variants of the <i>ycf1-rpl32</i> region, which normally includes the <i>ndhF</i> genes in the plastome, were identified, and some <i>Cymbidium</i> species contained at least two copies of that region in their organellar genomes. The four <i>ycf1-rpl32</i> variants seem to have a clear pattern of close relationships. Patterns of <i>ndh</i> degradation between closely related taxa and translocation of <i>ndh</i> genes to the chondriome in <i>Cymbidium</i> suggest that there have been multiple bidirectional intracellular gene transfers between two organellar genomes, which have produced different levels of <i>ndh</i> gene degradation among even closely related species.</p></div

    The information of mt-<i>ndh</i> genes assembled from NGS data.

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    <p>The information of mt-<i>ndh</i> genes assembled from NGS data.</p

    Taxa list for this study.

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    <p>Taxa list for this study.</p

    Alignment of <i>ndh</i> gene regions in both organellar genomes of <i>Cymbidium</i>.

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    <p>A red dotted-box indicates a plastome-like region in the chondriome. A) The plastid <i>ndhB</i> region from 44 bp downstream of 5′ end of gene was transferred to chondriome. At exon2 of mt-<i>ndhB</i>, a 132 bp deletion was found. B) The mt-<i>ndhJ-K-C</i> region contained a large deletion in and a large insertion in mt-<i>ndhK</i>. The length variation between two large insertions in mt-<i>ndhK</i> was caused by 28 bp tandem repeats. C) In contrast with deleted plastid <i>ndhF</i>, two types of mt-<i>ndhF</i> were found in both species. D) Both <i>ndhA</i> exon1 and <i>ndhH</i> were deleted in the plastome, whereas they were found in the chondriome of both species.</p

    Four types of <i>ycf1-rpl32</i> regions in organellar genomes of <i>Cymbidum</i> and closely related taxa.

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    <p>The red dotted line refers to identical position of C) the end of replaced <i>ycf1</i> and D) the end of deletion in <i>Acriopsis</i> and <i>Thecostele</i>. A) The <i>ndhF</i> genes of currently sequenced plastomes are divided into two groups. Type A is similar to <i>ndhF</i> of <i>Masdevallia coccinea</i> whereas type B has 420 bp <i>ycf1</i>-like region at 3′ region of <i>ndhF</i>. B) Type A <i>ycf1-rpl32</i> region is more conserved than the others. C) Type B <i>ycf1-rpl32</i> regions have a number of deletions. D) The 3′ region of <i>ndhF</i> is deleted in the type C <i>ycf1-rpl32</i> region. E) Type D <i>ycf1-rpl32</i> region completely lacks <i>ndhF</i>.</p

    Degradation patterns for 11 <i>ndh</i> genes in 743 angiosperm plastomes.

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    <p>To compare the <i>ndh</i> gene degradation patterns, the state of <i>ndh</i> genes was scored as follows. 1: in-frame gene, 2: pseudogene due to presence of substitutions or short insertion-deletion mutations, 3: highly truncated gene, 4: completely deleted gene. A line refers to the percentage of different <i>ndh</i> degradation patterns and the bar refers to the percentage of plastome sequences in orders among the 743 plastomes. The yellow, green and blue boxes represent monocotyledons, rosids and asterids, respectively.</p

    Alignment of <i>ndh</i> gene regions in <i>Dendrobium catenatum</i> and <i>Epipogium aphyllum</i>.

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    <p>A red dotted-box indicates a plastome-like chondriome region. The plastid <i>ndh</i> genes of <i>Sobralia callosa</i> were used as reference. A) In contrast with plastid <i>ndhJ-K-C</i> region of <i>D</i>. <i>catenatum</i>, mt-<i>ndhJ-K-C</i> region was similar to the reference in length with the exception of deletion in mt-<i>ndhK</i>. B) Both plastid and mt-<i>ndhF</i> of <i>D</i>. <i>catenatum</i> contained large deletions. C) The plastid region of <i>D</i>. <i>catenatum</i> from downstream of <i>rpl32</i> to downstream of 5′ end of <i>ndhG</i> was transferred to the chondriome. D) The <i>ndhI-A-H</i> region in the chondriome of <i>D</i>. <i>catenatum</i> has a mt-<i>ndhI-A</i> exon2 region that is inverted relative to the reference, whereas this region was completely deleted in the plastome. E) Plastome of <i>E</i>. <i>aphyllum</i> has completely deleted all 11 <i>ndh</i> genes, whereas its chondriome has retained an <i>ndhI-A</i> region; there was an inversion between 3′ region of <i>ndhI</i> and upstream of 5′ end <i>ndhA</i> exon2.</p

    Neighbour net for Asparagales and outgroups.

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    <p>Neighbour net for Asparagales and outgroups with uncorrected p-distances, based on 284 species using four plastid genes: <i>atpB</i>, <i>matK</i>, <i>ndhF</i>, and <i>rbcL</i>. Families and subfamilies circumscriptions follow APG III (2009) and Chase et al. (2009) are colour-coded. Scale bar, 0.01.</p

    Divergence time estimates for Asparagales, based on four cpDNA genes (atpB, matK, ndhF and rbcL).

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    <p>The maximum clade credibility tree from the divergence times estimated with BEAST. The 95% highest posterior density (HPD) estimates for each well-supported clade are represented by bars. Numbers at nodes are fossil calibration points: 93 Ma, age for the most recent common ancestor (MRCA) of extant Asparagales; 83.5 Ma, age for the MRCA of Zingiberales; 106.5±5.5 (93–120) Ma, age for the root of the tree (The upper age constraint of 120 Ma corresponds to the oldest known Monocot fossil). Detailed descriptions see the section of material and methods in text.</p
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