Identical Inverted Repeat Research Articles

Characterization of the complete chloroplast genome sequence of <i>Hypericum petiolulatum</i> (Hypericaceae)

<i>Hypericum</i> L. (Hypericaceae) is one of the best-selling herbal medicines in the world comprising ca. 500 species of herbs, shrubs, and small trees. <i>Hypericum petiolulatum</i> Hook. f. & Thomson ex Dyer is widely distributed in China, Vietnam, Myanmar, Nepal, India, Malaysia, and Bhutan and is used as a traditional herb to treat hemoptysis and inflammation. In this study, we sequenced and assembled the complete chloroplast (cp) genome of <i>H. petiolulatum</i>. The complete plastome of <i>H. petiolulatum</i> was 136,105 bp in length, with a large single copy region (LSC) of 93,709 bp, a small single copy region (SSC) of 11088 bp and two identical inverted repeats (IRs) of 15,654 bp. The overall GC content of the plastome was 37.0%, while GC contents of the LSC, SSC, and each IR were 35.5%, 31.0%, and 43.8%, respectively. In addition, 116 genes consisting of 76 protein-coding genes, six ribosomal RNA genes, and 34 transfer RNA genes were identified. A phylogenetic analysis of 14 taxa inferred based on cp genome sequences revealed a close relationship between <i>H. petiolulatum</i> and <i>H. perforatum</i>. The complete cp genome sequence of <i>H. petiolulatum</i> reported in this paper will facilitate population and phylogenomics studies of this medicinal plant group.

The complete chloroplast genome of Meconopsis bella Prain 1894 (Papaveraceae), a high-altitude plant distributed on the Qinghai-Tibet plateau

Meconopsis bella Prain 1894 (M. bella) is a rare herb within the family Papaveraceae of which unique and gorgeous purple flowers are blooming in the flowering phase. In this study, we reported the complete chloroplast (cp) genome of M. bella, which was mainly distributed on the Qinghai-Tibet plateau. The complete chloroplast genome sequence of M. bella was 153,073 bp in size and was characterized by a typical quadripartite structure consisting of a large single-copy (LSC) region of 83,562 bp, a small single-copy (SSC) region of 178,33 bp and two identical inverted repeats (IR) regions of 25,839 bp. The genome contained 133 genes, including 88 protein-encoding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis based on the maximum-likelihood (ML) method showed that M. bella was closely related to M. paniculate and M. pinnatifolia within the genus Meconopsis.

Characterization of the complete chloroplast genome sequence of Maesa japonica (Myrsinaceae)

Maesa Forssk. (Myrsinaceae) has approximately 200 species distributed in the tropics from southern Africa to East Asia. Among them, Maesa japonica (Thunb.) Moritzi ex Zoll. is distributed throughout China, Japan, Taiwan, Vietnam, and Korea. In Korea, this species is found only on Jejudo Island. In this study, we conducted whole-genome sequencing of M. japonica chloroplast (cp). The complete cp genome sequence of M. japonica was found to be 157,189 bp in length, consisting of large (87,780 bp) and small (18,143 bp) single-copy regions (LSC and SSC, respectively) and a pair of identical inverted repeats (IRs) (25,633 bp). The overall GC content of the cp genome was 38%, while those of the LSC, SSC, and each IR were 35.2%, 30.9%, and 43.1%, respectively. Furthermore, 130 genes consisting of 85 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes were identified in the cp genome. A phylogenetic analysis of 12 taxa inferred from the cp genome revealed a close relationship between M. salicifolia and M. japonica. The complete cp genome sequence of M. japonica provides valuable information for future evolutionary and phylogenetic studies of Maesa.

The complete chloroplast genome sequence of <i>Rhododendron caucasicum</i> (Ericaceae)

<i>Rhododendron caucasicum</i> Pall. is a shrub distributed in the mountainous areas of the Caucasus from northeastern Türkiye towards the Caspian Sea. This study reports the first complete chloroplast genome sequence of <i>R. caucasicum</i>. The plastome is 199,487 base pairs (bp) long and exhibits a typical quadripartite structure comprising a large single-copy region of 107,645 bp, a small single-copy region of 2,598 bp, and a pair of identical inverted repeat regions of 44,622 bp each. It contains 143 genes, comprising 93 protein-coding genes, 42 tRNA genes, and eight rRNA genes. The large chloroplast genome size is likely due to the expansion of inverted repeats. A phylogenetic analysis of chloroplast genomes with other <i>Rhododendron</i> species supports previously recognized infrageneric relationship.

The complete chloroplast genome sequence of <i>Dracocephalum rupestre</i> (Lamiaceae)

<i>Dracocephalum rupestre</i> Hance is a perennial herb distributed across China, Mongolia, and Korea. This study reports the first complete chloroplast genome sequence of <i>D. rupestre</i>. The plastome is 151,230 bp long and exhibits a typical quadripartite structure comprising a large single-copy region of 82,536 bp, a small single-copy region of 17,408 bp, and a pair of identical inverted repeat regions of 25,643 bp each. It contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of <i>D. rupestre</i> and related species of Lamiaceae showed that the genus <i>Dracocephalum</i> is a monophyletic group, and <i>D. rupestre</i> is most closely related to <i>D. psammophilum</i>.

Characterization of a Novel Complete-Genome Sequence of a Galliform Chaphamaparvovirus from a Free-Range Laying Chicken Clinically Diagnosed with Spotty Liver Disease.

This study reports a novel complete genome of galliform chaphamaparvovirus 4, which was detected in the bile of a free-range laying chicken diagnosed with spotty liver disease. The genome was 4,367 bp in length, enclosed by two identical inverted terminal repeats. The detection of this novel chaphamaparvovirus represents a notable concern for the poultry industry in Australia.

Characterization of the complete chloroplast genome of Clematoclethra scandens subsp. actinidioides (Actinidiaceae)

Clematoclethra scandens subsp. actinidioides (Actinidiaceae) is an endemic medicinal species in China. Here, we first sequenced and characterized the complete chloroplast genome of C. scandens subsp. actinidioides. The chloroplast genome was 159,341 bp in length, containing a large single-copy of 88,351 bp and a small single-copy of 21,580 bp separated by a pair of identical inverted repeat regions of 24,705 bp each. A total of 131 genes were identified, including 84 protein-coding genes, 39 tRNA, and eight rRNA genes. The phylogenetic analysis of C. scandens subsp. actinidioides showed a relatively close relationship with Clematoclethra scandens subsp. hemsleyi.

A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732.

Mutants of Micrococcus luteus strain ATCC49732 lacking the yellow pigment sarcinaxanthin were observed at an unexpectedly high frequency and the molecular basis was investigated. PCR probing revealed complete deletion of the crt biosynthetic operon in 11/14 mutants. Inverse PCR was used to identify a common breakpoint 35kb downstream from crt precisely at the end of the right inverted repeat (IRR) of a partial ISMlu8 element that lies between two inversely oriented full-length ISMlu2. A total of three different breakpoints 5' to crt were found with the sequence CTAG one bp 5' to each novel junction. Analysis of 35 genomic sites with single ISMlu8 insertions showed that ISMlu8 transposase has high specificity for CTAG, implicating its key role in formation of the Δcrt deletions. No downstream deletion endpoints were observed at an immediately adjacent ISMlu8 with a nearly identical IRR in the same orientation and slightly closer to the crt operon, indicating that access of ISMlu8 transposase to the ISMlu2-flanked ISMlu8 IRR is greatly enhanced by the surrounding oppositely oriented ISMlu2s. The association of high frequency genomic rearrangement with this distinctive natural configuration of ISs from two different IS families offers a new insight into IS element evolutionary potential.

Complete chloroplast genome of Euphorbia micractina Boiss (Euphorbiaceae: Euphorbia)

Euphorbia micractina Boiss is a plant with high medicinal value. Yet, its molecular biology is not fully understood. In this study, we sequenced the whole chloroplast genome (CP) sequence of E. micractina to study its phylogenetic relationship in Euphorbiaceae. The total length of the chloroplast genome of E. micractina is 162,056 bp, including a large single-copy (LSC) region of 89,936bp bp, a small single-copy (SSC) region of 18,376 bp, and a pair of identical inverted repeat regions (IRs) of 11,367 bp. The genome has 128 genes, including 84 protein-coding genes, 36 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The overall GC content of the plastome is 35.7%. The phylogenetic analysis of E. micractina with 30 related species suggested a closest taxonomical relationship with Euphorbia pekinensis in the Euphorbiaceae family.

The complete chloroplast genome of Echeveria lilacina Kimnach & Moran 1980 (Saxifragales: Crassulaceae)

Echeveria lilacina Kimnach & Moran 1980 is a succulent plant having ornamental and ecological importance. In this study, the first complete chloroplast genome of Echeveria lilacina, a species belonging to the Crassulaceae family, was characterized from the de novo assembly of Illumina NovaSeq 6000 paired-end sequencing data. The chloroplast genome of E. lilacina is 150,080 bp in length, which includes a large single-copy (LSC) region of 81,741 bp, a small single-copy (SSC) region of 16,747 bp, and a pair of identical inverted repeat regions (IRs) of 25,796 bp each. The genome annotation revealed a total of 138 genes, including 87 protein-coding genes, 41 transfer RNA (tRNA) genes, and 10 ribosomal RNA (rRNA) genes. The phylogenetic analysis with 15 complete chloroplast genome sequences including outgroup showed that E. lilacina formed the closest taxonomical relationship with Graptopetalum amethystinum in the Crassulaceae family.

Complete chloroplast genome characterization and phylogenetic analysis of Clematis mandshurica (Ranunculaceae)

The complete chloroplast genome sequence of Clematis mandshurica Ruprecht (1867), a specie of the Ranunculaceae family, and its phylogenetic relationships with other species have been reported in this study. The complete chloroplast genome of C. mandshurica is 159,563 bp in length, including a large single-copy (LSC) region of 79,360 bp, a small single-copy (SSC) region of 18,121 bp, and a pair of identical inverted repeat regions (IRs) of 31,041 bp. The genome encodes a total of 132 genes, including 90 protein-coding genes, 34 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis reveals that C. mandshurica was found to be closest to Clematis taeguensis. The complete chloroplast genome of C. mandshurica contributes to a better understanding of phylogenetic relationships among Clematis species.

The complete chloroplast genome of Bothriochloa ischaemum

Bothriochloa ischaemum (Linn.) 1936 is a high-quality perennial forage in Loess Plateau of China. In this study, we sequenced and characterized the complete chloroplast genome of B. ischaemum, which was a circular DNA of 138,316 bp in length, including a large single copy (LSC) region of 80,226 bp, a small single copy (SSC) region of 12,526 bp, and the circular DNA was separated by a pair of identical inverted repeat regions (IRs) of 22,782 bp each. A total of 134 genes were identified, including 87 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that B. ischaemum was closer to B. decipiens and B. alta, genus Bothriochloa was closely related to genus Pseudanthistiria. Our findings will be helpful for better understanding of genetic diversity of Bothriochloa plants.

The complete plastome of the South African species, Amaryllis belladonna L. (Amaryllidaceae)

The complete plastome sequence of Amaryllis belladonna L. is assembled and annotated. This is the type species of Amaryllis and therefore the type of the family Amaryllidaceae and as such, is important to document the phylogenetic position of the family. The plastome sequence has a length of 158,145 bp, with the large single copy (LSC) regions comprising 85,963 bp, the small single copy (SSC) 18634 bp and two identical inverted repeats (IR) regions each of 26,774 bp. Phylogenetic analysis fully resolved Amaryllis in a clade with Crinum L. in the Amaryllidoideae, as expected, with the Allioideae as a sister group. Agapanthus (Agapanthoideae) is a sister to the other two subfamilies in the Amaryllidaceae. The phylogenetic tree produced corresponds to previous topologies based on plastome molecular markers including matK, ndhF and rbcL. This is the first paper reporting the whole plastome comparison of the type genera of all three subfamilies in the Amaryllidaceae.

Complete chloroplast genome of Gypsophila oldhamiana Miq. (Caryophyllales: Caryophyllaceae)

The complete chloroplast genome sequence of Gypsophila oldhamiana Miq., a species of the Caryophyllaceae family, was assembled and analyzed from the de novo assembly of Illumina paired-end sequencing data. The total length of the chloroplast genome of G. oldhamiana was 152,675 bp including a large single-copy (LSC) region of 83,552 bp, a small single-copy (SSC) region of 17,349 bp, and a pair of identical inverted repeat regions (IRs) of 25,887 bp. The genome possessed a total of 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis of G. oldhamiana with 14 related species discovered the closest taxonomical relationship with Gypsophila vaccaria voucher in the Caryophyllaceae family.

Characterization of the complete chloroplast genome of Rhododendron henanense subsp. lingbaoense Fang

Rhododendron henanense subsp. lingbaoense is endemic in China. The cpDNA of R. henanense subsp. lingbaoense is a typical quadripartite structure with a length of 208,015 bp, including a large single-copy region of 110,593 bp and a small single-copy region of 2606 bp separated by a pair of identical inverted repeat regions of 47,408 bp each. The chloroplast genome contains 119 genes, including 86 protein-coding genes, four ribosomal RNA genes, and 29 transfer RNA genes. The phylogenetic analysis of R. henanense subsp. lingbaoense showed a relatively close relationship with Rhododendron delavayi.

Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae.

Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.

The complete chloroplast genome sequence of Michelia balansae var. balansae (Aug. Candolle) Dandy, a timber and spices species in Magnoliaceae

Michelia balansae var. balansae (Aug. Candolle) Dandy is a timber and spices species in Magnoliaceae, native to China and Vietnam. In this paper, the complete chloroplast genome (cpDNA) and basic annotated information were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of chloroplast genome of M. balansae var. balansae is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that M. balansae var. balansae is most affinal to M. montana and they form a nomophyletic group with other 14 Michelia species. This Michelia clade is sister to the Aromadendron clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.

Determination of chloroplast genome sequence of Magnolia ofeliae A. Vázquez & Cuevas (Magnoliaceae), an endangered Mexican Magnolia

Magnolia ofeliae A. Vázquez & Cuevas, a plant species endemic to south Jalisco, Mexico, is a critically endangered (CR) species based on the IUCN Red List. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of M. ofeliae was 159,839 bp including four subregions: a large single-copy (LSC) region of 88,027 bp and a small single-copy (SSC) region of 18,752 bp separated by a pair of identical inverted repeat regions (IRs) of 26,530 bp each. The GC content of the cp genome of M. ofeliae is 39.3%. The cp genome encoded a set of 113 genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results that M. ofeliae is a sister to all other magnolias in the subfamily Magnolioideae.

Characterization of the complete chloroplast genome of Ligusticum sinense, as a Chinese herb to treat toothache in China

Ligusticum sinense is a popular herb in Chinese medicine. The circular double-stranded complete chloroplast genome of L. sinense was 146,342 bp in length, exhibiting a typical quadripartite structure. It contained a large single-copy region (LSC) of 91,788 bp, a small single-copy region (SSC) of 17,618 bp and two identical inverted repeat (IR) regions of 18,468 bp each. The overall nucleotide composition of chloroplast genome sequence is: A (30.8%), T (31.6%), C (19.2%), G (19.4%) and the total G + C content of 38.6%. The chloroplast genome contained 127 genes, including 83 protein-coding genes, 36 transfer RNA genes and 8 ribosomal RNA genes were annotated. The total of 15 genes duplicated in one of the IR, including 6 tRNA, 4 rRNA, and 5 protein-coding genes. The ML phylogenetic tree indicated that L. sinense is closely related to L. tenuissimum in the phylogenetic relationship.

The complete chloroplast genome sequence of the Manglietia longirostrata Sima, a rare and endemic species to china

Manglietia longirostrata Sima is a rare and endemic species in China. The complete chloroplast genome (cpDNA) of M. longirostrata was sequenced and assembled in this study. The cpDNA is 160,049 bps in length, contains a large single-copy region (LSC) of 88,098 bp and a small single-copy region (SSC) of 18,861 bp, separated by a pair of identical inverted repeat (IR) regions of 26,571 bp, each. The genome contains 123 genes, including 73 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis of cp genome of M. longirostrata with 11 chloroplast genomes previously reported in the Magnoliaceae shows that M. longirostrata is close to Manglietia megaphylla with high bootstrap value.