Small Single-copy Region Research Articles

Phylogenomic Analysis of Dichrocephala benthamii and Comparative Analysis within Tribe Astereae (Asteraceae).

Dichrocephala benthamii C. B. Clarke has long been used as traditional Chinese medicine. However, the chloroplast (cp) genome of D. benthamii is poorly understood so far. In this study, we sequenced and analyzed the cp genome of D. benthamii. The results showed that the cp genome is 152,350 bp in length, with a pair of inverted repeat regions (IRa and IRb, each 24,982 bp), a large single-copy (LSC) region comprising 84,136 bp, and a small single-copy (SSC) region comprising 18,250 bp. The GC content of the cp genome was 37.3%. A total of 134 genes were identified, including 87 protein-coding genes (CDS), 38 tRNA genes, 8 rRNA genes, and 1 pseudogene (ycf1). Expansion or contraction of IR regions were detected in D. benthamii and other species of the tribe Astereae. Additionally, our analyses showed the types of sequence repeats and the highly variable regions discovered by analyzing the border regions, sequence divergence, and hot spots. The phylogenetic analysis revealed D. benthamii is the basal group of Astereae. The results of this study will be a significant contribution to the genetics and species identification related to D. benthamii.

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.

Estimation of the Genome Size and Complete Chloroplast Genome in Adenophora remotiflora: Genome Structures, Comparative Genomics, and Phylogenetic Diversity

Adenophora remotiflora is a wild perennial plant used as oriental medicine and ornamental flowers in East Asia. The haploid genome size of A. remotiflora was estimated at 3.9 Gb with a 2.42% heterozygosity ratio. The chloroplast genome of 174,455 base pairs (bp) shows a circular map structure, and has four conserved regions consisting of a large single-copy region of 108,423 bp, a small single-copy region of 10,444 bp, and a pair of inverted repeats (each 27,794 bp). A total of 108 unique genes were annotated, comprising 74 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. A total of 155 repeat sequences were identified, and comparative genome structures were characterized among the Adenophora species. Phylogenetic diversity showed that A. remotiflora is in a close position within the Adenophora genus, and Adenophora erecta is in the closest evolutionary position.

Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

BackgroundPrunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome.ResultsThe complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus.ConclusionsThe current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.

Characterization of chloroplast genome and phylogenetic analysis of the Elaeagnus hybrid variety E. ‘viridis’ (Elaeagnaceae)

Elaeagnus ‘viridis’, an artificial hybrid of E. macrophylla (♂) Thunb. (1784) × E. pungens (♀) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. ‘viridis’. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. ‘viridis’ is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.

The first complete chloroplast genome sequence of Pentaphragma spicatum Merr. (Pentaphragmataceae) and phylogenetic analysis

Pentaphragma spicatum Merr. is an endemic wild edible plant of China belonging to the Pentaphragmataceae family. It is widely consumed by Shangsi County resident in Guangxi Fangchenggang. Initially, Pentaphragma was classified as a genus within the Campanulaceae family, but, later it was treated as part of the Pentaphragmataceae family. However, the chloroplast genome of Pentaphragmataceae has not yet been reported. In this study, we sequenced the first complete chloroplast (cp) genome of P. spicatum from Guangxi, China. The whole genome was 154,229 bp in length, consisting of a pair of inverted repeats (IR each 25,572 bp), a large single-copy region (LSC 84,884 bp), and a small single-copy region (SSC 18,201 bp). The complete genome contained 129 genes, including 87 protein-coding genes, 34 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 37.71%. Based on a maximum-likelihood phylogenetic analysis, it has been determined that P. spicatum is not phylogenetically related to Campanulaceae and supports the decision to classify it as a separate family, Pentaphragmataceae. The complete chloroplast genome of P. spicatum will help enhance and integrate the existing genome data of Asterales. This will provide insights into the phylogenetic relationship within Campanulaceae.

The complete chloroplast genome of Goodyera yunnanensis Schltr.

The family Orchidaceae is renowned for its extensive diversity. Within this family, the genus Goodyera R. Br. is classified under the subtribe Goodyerinae, comprising approximately 99 species. In this study, a species Goodyera yunnanensis Schltr., its plastid genome was characterized. The plastid genome of G. yunnanensis is 146,197 bp in size and exhibits a typical quadripartite structure with a pair of inverted repeat regions (IRs) of 25,611 bp, a large single-copy region (LSC) of 81,300 bp and a small single-copy region (SSC) of 13,675 bp. A total of 126 genes were identified, containing 80 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The overall GC content is 37.2%, with corresponding values of 43.3%, 34.7% and 29.1% in IR, LSC and SSC regions, respectively. Forty-seven simple sequence repeats (SSRs) are found in G. yunnanensis plastome, and the frequency of mononucleotide repeats is significantly higher than other repeat types. Phylogenetic analysis indicates that Goodyera is resolved into four clades. G. yunnanensis belongs to the monophyletic clade A, and its phylogenetic position can be reasonably supported by morphological and molecular data.

The complete chloroplast genome sequence of Zygophyllum brachypterum (Zygophyllaceae) reveals its distinctive characteristics and evolutionary implication

Zygophyllum brachypterum Karelin & Kirilov belongs to Zygophyllaceae and is mainly distributed in the desert regions of Central Asia, Mongolia, and Northwest China. The species is valuable in exploring the adaptations of Zygophyllaceae plants to salt stress in ecological environments. In this study, we report the complete chloroplast (cp) genome of Z. brachypterum. The entire cp genome was 104590 bp in length, with a large single-copy region (LSC, 79170 bp), a small single-copy region (SSC, 16778 bp), and two inverted repeats (IRa/IRb) of 4321 bp each. A total of 106 genes were detected, among which seven were located in the IRs, and 65, 30, and 4 were protein-coding, tRNA, and rRNA genes, respectively. Notably, eleven genes encoding the subunits of NAD(P)H dehydrogenase complex (NDH) were absent. Phylogenetic analysis indicated that Z. brachypterum belonged to Zygophylloideae (Zygophyllaceae). Furthermore, it was closely related to Z. fabago and Z. kansuense.

The complete chloroplast genome sequence of Ludwigia adscendens (L.) Hara, 1953 (Onagraceae)

Ludwigia adscendens (L.) Hara, 1953 (L. adscendens) belongs to the family Onagraceae, which is a traditional medicinal plant distributed worldwide. In this study, the first complete chloroplast genome of L. adscendens was sequenced and assembled. The assembled chloroplast genome of L. adscendens is 159,560 bp in length, containing a pair of inverted repeat region A (IRA) of 24,762 bp, inverted repeat region B (IRB) of 24,762 bp, separated by a large single-copy (LSC) sequence of 90,276 bp and a small single-copy (SSC) region of 19, 760 bp, respectively. A total of 129 genes were annotated in the entire chloroplast genome, consisting of 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 84 protein-coding genes, with a total GC content of 37.27%. The phylogenomic analysis showed that L. adscendens was closely related to L. octovalvis in the Onagraceae family. Further evolutionary studies of the genus Ludwigia could benefit from the complete chloroplast genome of L. adscendens present in this study and the obtained results would provide useful information for future phylogenetic, taxonomic, and evolutionary studies on Onagraceae.

The complete chloroplast genome of Ziziphus mairei Dode 1908 (Rhamnaceae), an endangered perennial plant in Yunnan, China

Ziziphus mairei Dode 1908 (Rhamnaceae) is a rare and endangered perennial plant in Yunnan, China. In this study, we sequenced, assembled, and annotated the complete chloroplast genome of Z. mairei. The complete chloroplast genome was a closed circular molecule of 161,546 bp with a typical tetrad structure, containing a large single-copy (LSC) region of 89,252 bp, a small single-copy (SSC) region of 19,364 bp, and a pair of inverted repeat (IR) regions of 26,465 bp. A total of 128 genes have been annotated, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content is 36.7%. Phylogenetic analysis revealed that Z. mairei is closely related to Z. hajarensis, Z. jujuba, and Z. jujuba var. spinosa. Our results provide useful genetic resources for further studies on the conservation and evolution of Z. mairei.

The complete chloroplast genome sequence of Rosa ‘Limoncello’ (Rosales: Rosaceae)

Rosa ‘Limoncello’ finds applications in gardening and landscaping. In this study, we assembled and annotated the complete chloroplast genome of this variety for the first time. The length of its chloroplast genome was 156,493 bp, containing two short inverted repeat regions of 26,052 bp, each separated by a large single-copy region of 85,649 bp and a small single-copy region of 18,740 bp. The chloroplast DNA of R. ‘Limoncello’ consisted of 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. On comparing the complete chloroplast sequence of R. ‘Limoncello’ with that of other Rosa species, R. ‘Limoncello’ was found to be closely related to Rosa cymosa. Thus, information on the chloroplast genome sequence of this rose variety can facilitate phylogenetic studies of the genus Rosa.

The complete chloroplast genome of Hordeum marinum ssp. marinum

Hordeum marinum ssp. marinum (Huds.) R. J. Soreng (2003) is a halophyte wild relative of barley and wheat, which exhibits remarkable salt tolerance characteristics. In this study, we presented the first characterization of the complete chloroplast genome of H. marinum ssp. marinum. Our findings reveal that the chloroplast genome of H. marinum ssp. marinum consists of a small single-copy region (SSC: 12,715 bp), a large single-copy region (LSC: 81,130 bp), and a pair of inverted repeat regions (IRs: 21,517 bp), amounting to a total length of 136,989 bp. The chloroplast genome encodes 139 genes, including 91 protein-coding genes, 38 tRNA genes, and ten rRNA genes. By utilizing phylogenetic analysis, we determine the evolutionary position of H. marinum in Triticeae. Our study provides valuable insights into the chloroplast genome of H. marinum ssp. marinum, which may have important implications for the improvement of cereal crops.

Characterization of the chloroplast genome of the marine microalga Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980

Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980, a costal green microalga, is considered as a promising animal feed in aquaculture due to the high content of fatty acids and carotenoid. Furthermore, T. marina plays important roles in bioremediation. In this study, we assembled the complete chloroplast genome of T. marina. Results showed that the full length of the complete chloroplast genome was 96,151 bp, containing a large single-copy region of 62,574 bp, a small single-copy region of 1261 bp, and a pair of inverted repeat regions of 16,158 bp. The GC content of the genome was 36.6%. A total of 125 genes were annotated, including 81 protein coding genes, 38 tRNA genes, and six rRNA genes. Phylogenetic analysis based on 22 chloroplast genomes suggested that T. marina was closely related to Tetraselmis sp. CCMP 881.

Chloroplast Genome Sequences and Phylogenetic Analysis of Eight Newly Sequenced Caryophyllaceae Species.

Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species. Using next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams, and S. lhassana (Williams) Majumdar. Bioinformatic software was used to conduct the comparative genome and phylogeny analysis of these cp genomes. The eight cp genomes were 132 188-151 919 bp in length, containing 130-132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, theinverted repeat (IR) boundaries of S. caespitella, S. atsaensis, S. lhassana, and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus. These results have provided new evidence and useful information for species identification, evolution, and genetic research on the Caryophyllaceae. In this study, eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.

New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes

Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958–84,792 bp), a small single-copy (SSC) region (18,585–18,768 bp), and a pair of inverted repeats (IRs) (25,058–25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.

Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae).

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes-trnK-UUU, infA, and rps16-were lost, and three genes-rps7, rpl23, and rpl32-were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.

Complete chloroplast genome of Rorippa apetala Y.Y. Kim & B.U. Oh (Brassicales: Brassicaceae), a species endemic to the Korean Peninsula

Here, we successfully assembled the complete chloroplast genome of Rorippa apetala Y.Y. Kim & B.U. Oh, a species endemic to the Korean Peninsula. The chloroplast genome was 154,818 bp long and exhibited a typical quadripartite structure comprising large single-copy (83,847 bp) and small single-copy (18,023 bp) regions, and a pair of inverted repeats (26,474 bp each). A total of 129 genes were encoded, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on the concatenated sequences of 78 protein-coding genes from 25 species revealed a close relationship between R. apetala and Rorippa indica (L.) Hiern, supported by full bootstrap value (100). Future studies employing more informative markers and a broader range of taxa will provide valuable insights into the biogeographical distribution of the genus Rorippa and offer a deeper understanding of the speciation process in R. apetala.

The complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890 (Chloranthaceae)

In this study, we sequenced and assembled the complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890. The total length of the complete chloroplast sequence was found to be 158,002 bp. It consisted of a large single-copy (LSC) region of 87,127 bp, a small single-copy (SSC) region of 18,541 bp, and a pair of inverted repeat (IR) regions, each with a length of 26,167 bp. The overall GC content of the complete chloroplast genome was 38.9%, with the LSC region, SSC region, and IR regions exhibiting GC contents of 37.4%, 34.1%, and 43.1%, respectively. The annotation of the chloroplast genome revealed a total of 131 genes, comprising 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that the seven sampled species of Chloranthus were divided into two clades. Within the clade characterized by long filamentous anther connectives, C. nervosus showed the closest relation to C. japonicus. These findings validated the previous preliminary results on the phylogenetic relationships of the seven species of Chloranthus with strong support.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus chingii Hu 1925 from the family Rosaceae

Rubus chingii Hu 1925 is an important medicinal vine shrub in the Rosaceae family, widely distributed in China and Japan. In this study, the complete chloroplast genome of R. chingii was sequenced and identified. The chloroplast genome was 155,563 bp in size with a total GC content of 37.06%. Two 25,749-bp inverted repeat (IRA and IRB) regions divided the genome as four sections, with the remainder forming a large single-copy (LSC, 85,322 bp) and a small single-copy (SSC, 18,743 bp) regions. This genome contained a total of 131 genes, of which 86 were protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that R. chingii, along with several other R. longisepalus, R. tsangii, R. hirsutus, R. taiwanicola, R. rubroangustifolius, and R. glandulosopunctatus, formed the monophylic group. Interestingly, the chloroplast genome structure we reported was different from the previously reported structure and provided richer phylogenetic analysis information in the Rubus genus compared to previous studies. The genome information reported in this paper will provide some useful information for further investigation on the evolution of the family Rosaceae.

Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae)

The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.