Copies Of Inverted Repeat Research Articles

The complete chloroplast genome and phylogenetic analysis of Stewartia sichuanensis (Theaceae), a Chinese endemic tree with narrow distribution

Stewartia sichuanensis is a rare plant species of Theaceae and is endemic to China. Its distribution area is highly restricted, and genomic information is extremely limited. The present study reports the first complete chloroplast of S. sichuanensis. The chloroplast genome length was 158,903 bp, with a GC content of 37.3%. The chloroplast genome was comprised of an 87,736 bp long large single copy (LSC), an 18,435 bp long small single copy (SSC), and two copies of inverted repeat (IR) regions of 26,366 bp. It contained 129 genes, including 85 encoding, 36 transfer RNA, and eight ribosomal RNA genes. The phylogenetic analysis suggested that S. sichuanensis was closely related to S. laotica and S. pteropetiolata.

The complete chloroplast genome of Gynura japonica and its phylogenetic implications

Gynura japonica (Asteraceae) is a folk herbal medicine with multi-pharmacological functions involving analgesic, hemostatic and antiangiogenic activities. The study was conducted to assemble the complete chloroplast (cp) genome of G. japonica through a genome-skimming approach. The assembled cp genome was 151,023 bp in size, with 62.8% AT content, consisting of a large single copy (LSC) of 83,185 bp, two copies of inverted repeat (IRa and IRb) of 24,847 bp, and a small single copy (SSC) of 18,144 bp. The cp genome of G. japonica contained 133 genes, including eight ribosomal RNA genes (rRNAs), 37 transfer RNA genes (tRNAs), 86 protein-coding genes (PCGs), and two pseudogenes (ψycf1 and ψrps19). Our phylogenomic analysis based on whole plastid genomes strongly supports G. japonica is a sister to the clade including Crassocephalum crepidioides and Jacobaea vulgaris.

Characterization of the complete chloroplast genome sequence of Cardamine lyrata Bunge(Brassicaceae)

Cardamine lyrata Bunge 1833 grows near paddy fields, streams and shallow water. Its young stems and leaves can be eaten. It can also be used as medicine and has the effect of clearing away heat and dampness. The complete chloroplast genome sequence of the C. lyrata was determined and assembled. The complete genome is 155,170 bp in length, including a large single-copy region (LSC) of 84,270 bp, a small single-copy region (SSC) of 17,918 bp and two copies of inverted repeat (IR) regions of 26,491 bp. The overall GC content of C. lyrata is 36.2%. The genome of C. lyrata contains 131 genes, including 85 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Phylogenetic analysis suggested that the ten species in Cardamine were clustered together into a single branch within the Brassicaceae family and C. amariformis is at the base of the tree and C. lyrata and C. fallax are sister groups of the inner clade.

The complete chloroplast genome of Chimonobambusa angustifolia C. D. Chu et C. S. Chao, a fiber and bamboo shoot species in Poaceae

Chimonobambusa angustifolia is a famous ornamental and edible bamboo species. Here, the complete chloroplast (cp) genome of C. angustifolia was assembled and annotated. The cp genome is 139,611 bp in size, consisting of two copies of inverted repeat (IR) regions of 21,799 bp, one large single-copy (LSC) region of 83,202 bp, and one small single-copy (SSC) region of 12,811 bp. It encodes 133 genes (110 unique), including 86 protein-coding genes (77 unique), 39 tRNA genes (29 unique), and 8 rRNA genes (4 unique). Phylogenetic analysis based on 21 cp genome sequences within four genera of family Poaceae indicated that genus Chimonobambusa were closely related to genus Shibataea, both belong to subtribe Shlbataeinae.

The complete chloroplast genome sequence of chaya (Cnidoscolus aconitifolius) and phylogenetic analysis

Cnidoscolus aconitifolius is a leafy green heathy vegetable and medicinal plant belongs to the family Euphorbiaceae. In the present study, we sequenced the complete chloroplast genome of C. aconitifolius, which is 158,658 bp in length and consisted of two copies of inverted repeat (IR) of 26,982 bp separated by a large single copy (LSC) of 87,022 bp and a small single copy (SSC) of 17,672 bp. The GC content of C. aconitifolius was 36.3%. A total of 130 genes were predicted, including 86 protein-coding genes, 36 tRNAs and 8 rRNAs. The plastid phylogenomic analysis support C. aconitifolius is closely related to Manihot esculenta.

The complete chloroplast genome sequence of Quercus sessilifolia Blume (Fagaceae)

Quercus sessilifolia Blume is one of the dominant tree species in East Asian evergreen broadleaved forests. In this study, we assembled and characterized the plastome of Q. sessilifolia using Illumina paired-end data. The circular genome is 160,813 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,862 bp, one large single-copy (LSC) region of 90,218 bp, and one small single-copy (SSC) region of 18,871 bp. It encodes a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 28 chloroplast genome sequences indicated that Q. sessilifolia was most closely related to Q. myrsinifolia with 90% bootstrap support.

Complete chloroplast genome of Sphagnum subsecundum Nees from Korea

We determined the complete chloroplast genome sequence of the peatmoss Sphagnum subsecundum Nees from Mt. Halla in Korea. The total size of the chloroplast genome was 140,136 bp, and it consisted of a large single-copy region (LSC) of 98,064 bp, a small single-copy region (SSC) of 21,388 bp, and two copies of inverted repeat (IRa and IRb) regions of 10,342 bp each. The genome encoded a set of 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This species formed a monophyletic clade with S. orientale and S. lenese as the result of ML phylogenetic analysis based on whole gemone sequence of 15 species including one outgroup species.

Characterization of the complete chloroplast genome of Quercus acrodonta (Fagaceae)

Quercus acrodonta Seemen is an East Asian evergreen oak tree species belonging to the Quercus section Ilex. Here, we assembled and annotated the complete chloroplast (cp) genome of the species. The circular genome is 161,105 bp in size, presenting a typical quadripartite structure including two copies of inverted repeat (IR) regions (25,864 bp), one large single-copy (LSC) region (90,357 bp), and one small single-copy (SSC) region (19,020 bp). A total of 131 genes are encoded, including 85 protein-coding genes (PCGs), 38 tRNAs, and eight rRNAs. Phylogenetic analysis based on cp genome sequences of 18 Quercus species indicated that Q. acrodonta was more closely related to Q. phillyraeoides.

The complete chloroplast genome sequence of Gynandropsis gynandra (Cleomaceae)

Gynandropsis gynandra (L.) Briquet is a monoecious herb species in the family Cleomaceae. It is an important commercial crop with medicinal and nutritional values. Here, we sequenced, assembled, and analyzed the complete chloroplast genome of G. gynandra. The circular genome is 158,152 bp in size, consisting of two copies of inverted repeat (IR) regions of 26,181 bp, one large single-copy (LSC) region of 87,242 bp, and one small single-copy (SSC) region of 18,548 bp. The overall GC content was 35.81%. A total of 131 genes were annotated, including 37 tRNA genes, 87 protein-coding genes, and seven rRNA genes. Phylogenetic analysis based on 10 chloroplast genome sequences indicated that G. gynandra was more closely related to Tarenaya hassleriana.

The complete chloroplast genome of the desert shrub Nitraria sphaerocarpa (Nitrariaceae) and phylogenetic analysis

Nitraria sphaerocarpa Maxim. is a typical desert shrub commonly used as a sand binder. Here, we sequenced and characterized the whole plastid genome of N. sphaerocarpa. It is 159,369 bp in length, containing two copies of inverted repeat (IR) regions (26,566 bp, each), a large single-copy (LSC) region (87,854 bp), and a small single-copy (SSC) region (18,383 bp). It has 114 unigenes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes, and one pseudogene (infA). Phylogenetic analysis shows that N. sphaerocarpa is located at a basal position of the genus Nitraria.

Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae).

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica, which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN/dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri, Hepatica americana, and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis.

Characteristic and phylogenetic analyses of chloroplast genome for Syringa komarowii C.K.Schneid. (Oleaceae) from Huoditang, China, an important horticultural plant

The genus Syringa (Oleaceae) comprises some of the most important cultivated horticultural trees worldwide. Syringa komarowii, is one of these important horticultural plants. We sequenced the complete chloroplast (cp) genomes of S. komarowii (previously identified as var. reflexa) using Illumina Hiseq X Ten platform. The cp genome exhibits a typical quadripartite structure with 158,020 bp in length, which consists of two copies of inverted repeat (IR) regions (25,676 bp) separated by a large single copy (LSC) region (87,628 bp) and a small single copy (SSC) region (19,040 bp). The cp genome of S. komarowii encodes a total of 132 genes, including 88 protein-coding genes, 36 tRNA genes and 8 rRNA genes. A maximum likelihood (ML) phylogenetic analysis resolved that S. komarowii in a clade with S. wolfii and S. yunnanensis. The ML tree also showed Syringa appeared more closely related to Ligustrum than to the other genera in the Oleaceae.

Characteristic and phylogenetic analyses of chloroplast genome for Ephedra monosperma (Ephedraceae), an important medicinal species

Ephedra monosperma is an important medicinal plant of Ephedra (Ephedraceae). The complete chloroplast genome of E. monosperma was assembled from Illumina pair-end sequence reads. The whole chloroplast (cp) genome is 109,548 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (20,398) separated by a large single copy (LSC) region (60,674 bp) and a small single copy (SSC) region (8078 bp). The cp genome of E. monosperma encodes a total of 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of E. monosperma cp genome is 36.6%. A maximum likelihood (ML) phylogenetic analysis revealed that E. monosperma was close to Ephedra equisetina. The ML tree also showed Ephedraceae appeared more closely related to Gnetaceae than to the other families in Gymnospermae.

Characterization of the complete plastid genome of Lysimachia christinae Hance (Primulaceae)

Lysimachia christinae Hance is widely distributed in subtropical China at the elevational range from 500–2300 m. The species is an important medicinal herb for treating jaundice, urinary disorders, and the liver. Here, we sequenced and characterized the whole plastid genome of L. christinae. It is 154,810 bp in length, containing two copies of inverted repeat (IR) regions (26,034 bp, each), a large single-copy (LSC) region (84,809 bp), and a small single-copy (SSC) region (17,933 bp). It has 114 genes, of which 80 are protein-coding, 30 are tRNA, and 4 are rRNA genes. The ML tree indicates L. christinae is closely related to Lysimachia congestiflora Hemsl. This genome information can help us better construct a backbone phylogeny of Lysimachia in the future.

Characterization of the plastome of Camellia pingguoensis (Theaceae), an endangered and endemic yellow camellia species in China

Camellia pingguoensis D. Fang is a shrub which is found on limestone of karst forests in Guangxi, China. In this study, we characterized the whole plastid genome of C. pingguoensis using Illumina paired-end sequencing reads. The plastome is 156,621 bp in length, containing two copies of inverted repeat (IR) regions (26,046 bp), a large-single copy (LSC) region (86,289 bp), and a small-single copy (SSC) region (18,240 bp). A total of 114 unique genes in the genome has 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic result indicates C. pingguoensis is closely related to C. nitidissima C. W. Chi.

Characterization of the complete plastid genome of Camellia amplexicaulis (Theaceae)

Camellia amplexicaulis (Pit.) Cohen-Stuart is a shrub or small tree that extensively cultivated throughout Vietnam and beyond, which is now considered to extinct in the wild. Here, the whole plastid genome of C. amplexicaulis was assembled using Illumina paired-end sequencing reads. The plastid genome is 157,203 bp in length with a typical quadripartite structure, containing two copies of inverted repeat (IR) regions (26,133 bp), a large-single copy (LSC) region (86,644 bp), and a small-single copy (SSC) region (18,293 bp). A total of 114 unique genes were encoded, of which 80 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The phylogenetic result indicates C. amplexicaulis is closely related to Camellia szechuanensis C. W. Chi.

The complete chloroplast genome sequence of Toxicodendron sylvestre (Anacardiaceae)

Toxicodendron sylvestre (Siebold & Zucc.) Kuntze is a deciduous tree species in the poison ivy genus of the sumac family. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of T. sylvestre. The circular genome is 159,600 bp in length, including two copies of inverted repeat (IR) regions of 26,465 bp, one large single-copy (LSC) region of 87,630 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 4 rRNA genes. Phylogenetic analysis based on 17 cp genome sequences revealed that T. sylvestre was more closely related to T. succedaneum.

The complete chloroplast genome of Clematis fruticosa Turcz. (Ranunculaceae)

Clematis fruticosa Turcz. is an erect shrubby plant with important ecological and economical value, which usually occurs in dry or desert areas. The complete chloroplast genome of C. fruticosa was assembled from Illumina pair-end sequence reads. The whole plastome is 159,684 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (31,045), a large single copy (LSC) region (79,461 bp) and a small single copy (SSC) region (18,133 bp). The plastome of C. fruticosa encodes a total of 137 genes, including 92 protein-coding genes, 1 pseudogene, 36 tRNA genes and 8 rRNA genes. The overall GC content of C. fruticosa plastome is 38.0%. A maximum likelihood (ML) phylogenetic analysis revealed that C. fruticosa was collectively sister to a clade of Clematis tangutica and Clematis aethusifolia with high support.

The complete chloroplast genome sequence of Quercus stewardiana (Fagaceae)

Quercus stewardiana A.Camus is an East Asian evergreen oak tree species belonging to Quercus section Cyclobalanopsis. In this study, we assembled and annotated the complete chloroplast (cp) genome of the species. The circular genome is 160,842 bp in size, presenting a typical quadripartite structure including two copies of inverted repeat (IR) regions (25,823 bp), one large single-copy (LSC) region (90,294 bp), and one small single-copy (SSC) region (18,902 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 cp genome sequences of 35 Fagaceae species indicated that Q. stewardiana was more closely related to Q. myrsinifolia.

The complete plastid genome sequence of Quercus ciliaris (Fagaceae)

Quercus ciliaris C.C.Huang & Y.T.Chang is one of the dominant tree species in the subtropical evergreen broad-leaved forests of China. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The circular genome is 160,842 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,823 bp, one large single-copy (LSC) region of 90,294 bp, and one small single-copy (SSC) region of 18,902 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 cp genome sequences of 35 Fagaceae species indicated that Q. ciliaris was among the members of section Cyclobalanopsis, and was most closely related to Q. myrsinifolia.