Copies Of Inverted Repeat Research Articles

The complete chloroplast genome sequence of Toxicodendron succedaneum (Anacardiaceae)

Toxicodendron succedaneum (L.) Kuntze is a deciduous and dioecious tree species in the family Anacardiaceae with important economic values. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of T. succedaneum. The circular genome is 159,710 bp in size, and presents a quadripartite structure including two copies of inverted repeat (IR) regions of 26,524 bp, one large single-copy (LSC) region of 87,622 bp, and one small single-copy (SSC) region of 19,040 bp. It encodes a total of 113 unique genes, including 80 protein-coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 16 cp genome sequences revealed that the genus Toxicodendron is closely related to Pistacia and Rhus, and T. succedaneum was most closely related to T. vernicifluum.

The complete chloroplast genome of Elsholtzia densa var. ianthina (Lamiaceae)

Elsholtzia densa var. ianthina has important medicinal valve and is used as Tibetan medicine. The complete chloroplast genome of E. densa var. ianthina was assembled from Illumina pair-end sequence reads. The whole plastome is 149,118 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (25,167) separated by a large single copy (LSC) region (81,411 bp) and a small single copy (SSC) region (17,373 bp). The plastome of E. densa var. ianthina encodes a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of E. densa var. ianthina plastome is 37.9%. A maximum likelihood (ML) phylogenetic analysis revealed that E. densa var. ianthina was related to Elsholtziasplendens.

The complete chloroplast genome sequence of Distylium macrophyllum (Hamamelidaceae)

Distylium macrophyllum H.T.Chang is a critically endangered tree species endemic to southern China. In this study, we assembled and characterized the plastome of D. macrophyllum using Illumina paired-end data. The circular genome is 159,089 bp in size, consisting of two copies of inverted repeat (IR) regions of 26,235 bp, one large single-copy (LSC) region of 87,822 bp, and one small single-copy (SSC) region of 18,797 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 13 cp genome sequences indicated that D. macrophyllum was sister to the clade of D. tsiangii and Parrotia subaequalis.

The complete chloroplast genome sequence of Quercus myrsinifolia (Fagaceae)

Quercus myrsinifolia Blume is an evergreen oak tree species native to East Asia, and is also one of the dominant trees of subtropical evergreen broad-leaved forests. In this study, we sequenced and analysed the complete chloroplast (cp) genome of the species. The circular genome is 160,803 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,840 bp, one large single-copy (LSC) region of 90,223 bp, and one small single-copy (SSC) region of 18,900 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 30 cp genome sequences indicated that Q. myrsinifolia was among the members of section Cyclobalanopsis, and was most closely related to Q. sichourensis.

The complete chloroplast genome sequence of Morella salicifolia (Myricaceae): characterization and phylogenetic analysis

Morella salicifolia (Myricaceae) is a dioecious plant of medicinal value. This study sequenced the complete chloroplast genome sequence of Morella salicifolia, the second to be sequenced in Myricaceae. The genome is 159,010 bp in size, composed of two copies of inverted repeat (IR) regions (26,045bp each) separating a large single-copy (LSC) region (88,207bp) from the small single-copy (SSC) region (18,713bp). The genome has 112 genes (77 protein-coding, 4 rRNA, and 31 tRNA) and an overall GC content of 36.2%. Phylogenetic relationship clustered M. salicifolia with M. rubra and Myricaceae clustered with Juglandaceae.

Characterization of the complete plastid genome of Quercus tarokoensis

Quercus tarokoensis is an endemic species to Taiwan, China. The complete plastid genome of Q. tarokoensis was assembled from Illumina pair-end sequence reads. The whole plastome was 161,355 bp in length and presented a quadripartite structure consisting of two copies of inverted repeat (IR) regions (25,860) separated by a large single copy region (90,602 bp) and a small single copy region (19,033 bp). The plastome of Q. tarokoensis encoded a total of 134 genes, including 86 protein-coding genes (79 PCG species), 40 tRNA genes (33 tRNA species), and 8 rRNA genes (4 rRNA species). The overall GC content of Q. tarokoensis plastome is 36.8%. A maximum likelihood phylogenetic analysis based on 33 complete plastomes revealed that Q. tarokoensis was collectively sister to a clade of (Quercus variabilis, (Quercus dolicholepis, Quercus baronii)) with high support.

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.

The complete chloroplast genome of Quercus baronii (Quercus L.)

Quercus baronii is an endemic species to China. The total length of the Q. baronii chloroplast genome is 161 072 bp. It exhibits typical quadripartite structure, composed of two copies of inverted repeat (IR) regions (25 843 bp), large single copy (LSC) region (90 341 bp), and small single copy (SSC) region (19 045 bp). The genome contains 134 genes, including 86 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed its relationship with reported Quercus L. species.

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be highly variable in size, gene content and order, repetitive DNA, and codon usage. Several unique plastome rearrangements include the disruption of two highly conserved operons (S10 and rps2-atpA), and the inverted repeat (IR) region in M. speciosa does not contain all genes in the ribosomal RNA operon. The sequence of M. speciosa is unusually small (128,787 bp); among angiosperm plastomes sequenced to date, only those of nonphotosynthetic species and those that have lost one IR copy are smaller. In contrast, the plastome of P. hortorum is the largest, at 217,942 bp. These genomes have experienced numerous gene and intron losses and partial and complete gene duplications. Some of the losses are shared throughout the family (e.g., trnT-GGU and the introns of rps16 and rpl16); however, other losses are homoplasious (e.g., trnG-UCC intron in G. palmatum and M. speciosa). IR length is also highly variable. The IR in P. hortorum was previously shown to be greatly expanded to 76 kb, and the IR is lost in E. texanum and reduced in G. palmatum (11 kb) and M. speciosa (7 kb). Geraniaceae plastomes contain a high frequency of large repeats (>100 bp) relative to other rosids. Within each plastome, repeats are often located at rearrangement end points and many repeats shared among the four Geraniaceae flank rearrangement end points. GC content is elevated in the genomes and also in coding regions relative to other rosids. Codon usage per amino acid and GC content at third position sites are significantly different for Geraniaceae protein-coding sequences relative to other rosids. Our findings suggest that relaxed selection and/or mutational biases lead to increased GC content, and this in turn altered codon usage. We propose that increases in genomic rearrangements, repetitive DNA, nucleotide substitutions, and GC content may be caused by relaxed selection resulting from improper DNA repair.

Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria.

In the mitochondria of Tetrahymena pyriformis ST, the large subunit ribosomal RNA (LSU rRNA) is discontinuous, consisting of two species, alpha (280 nucleotides in length) and beta (approximately equal to 2.45 kilobases long). LSU alpha is the 5'-terminal portion (i.e. a 5.8 S-like rRNA), and LSU beta constitutes the rest of this LSU rRNA, as judged by both primary and secondary structure homology to other LSU rRNAs. Remarkably, LSU alpha is encoded downstream of LSU beta, the two genes being separated by a tRNALeu gene. This is the first demonstration of a discontinuous rRNA whose coding sequences are rearranged, deviating from the conventional, highly conserved, 5'----3' order of sequence domains in the LSU rRNA gene. This novel gene organization (5'-LSU beta-2-base pair spacer-tRNALeu-10-base pair spacer-LSU alpha) is identical in both copies of the subterminal inverted repeat in the linear T. pyriformis mitochondrial genome. Sequence heterogeneity in the LSU alpha transcript and its genes, together with Northern hybridization data, suggest that both copies of the inverted repeat are expressed.