Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress.

The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03328-7.

Complete chloroplast genome of Baccaurea ramiflora and its phylogenetic analysis.

Baccaurea ramiflora Lour. is a popular tropical fruit tree, mainly grown in Myanmar, India, and other tropical or sub-tropical regions where it is commonly referred to as Myanmar grapes, Burmese grapes, or Latkan, respectively. Besides food, B. ramiflora is a traditional medicinal plant with several pharmaceutical effects. It is also a crucial component of Chinese Dai medicine. Here, the chloroplast genome of B. ramiflora was sequenced, assembled, and annotated. The complete chloroplast genome is 161,093 bp in length with a GC content of 36.71%. Additionally, it comprises a large single-copy region (LSC) of 89,503 bp, a small single-copy region (SSC) of 18,818 bp, and two inverted repeat regions (IRa and IRb) of 26,386 bp. In total, 128 genes were annotated, including 82 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. Phylogenetic analysis revealed that B. ramiflora is closely related to Phyllanthus emblica, Glochidion chodoense, and Phyllanthus amarus. This study provides useful genomic information for future phylogenetic studies of B. ramiflora and Phyllanthaceae family.

The complete chloroplast genome and phylogenetic analysis of Artocarpus champeden.

Artocarpus champeden Spreng. is a popular fruit tree, grown in tropical and subtropical regions. Besides food, A. champeden is also a medicinal plant with various medicinal properties. In this study, A. champeden chloroplast genome was sequenced, assembled, and annotated due to its rich information on species evolution and inter-species genetic relationships. The quadripartite structure of A. champeden complete chloroplast genome is 158,568 bp in length and comprises a large single-copy region (LSC) of 88,076 bp, a small single-copy region (SSC) of 19,028 bp, and two inverted repeat regions (IRa and IRb) of 25,732 bp. A total of 131 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. Phylogenetic analysis revealed a close relationship between A. champeden and A. heterophyllus. In addition, the study provides abundant genomic information for future phylogenetic studies of A. champeden and the Moraceae family.

Complete chloroplast genome sequence and phylogenetic analysis of dragon fruit (Selenicereus undatus (Haw.) D.R.Hunt).

Selenicereus undatus (Haw.) D.R.Hunt is a member of the family Cactaceae. The chloroplast genome of S. undatus was sequenced, assembled, and annotated in the present study. The chloroplast genome was 133,326 bp in length, consisting of a typical quadripartite circle: a large single-copy region of 68,256 bp, two inverted repeat regions of 21,677 bp, and a small single copy region of 21,716 bp. A total of 120 predicted genes were identified, and a maximum likelihood was constructed, placing S. undatus as the sister taxon of Lophocereus schottii and Carnegiea gigantea, other members of the family Cactaceae.

The complete chloroplast genome and phylogenetic analysis of Nephelium lappaceum (rambutan).

Nephelium lappaceum is a popular tropical fruit belonging to the Sapindaceae family. The plant originated in Malaysia and Indonesia and is commonly called rambutan. Because of its refreshing flavor and exotic appearance, rambutan is widely accepted in the World. Due to its significant medicinal properties, the fruit has also been employed in traditional medicine for centuries. The chloroplast genome of rambutan was sequenced, assembled, and annotated in the present study. The chloroplast genome length was 161,356 bp and contained 132 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. It possessed the typical quadripartite circle structure with a large single-copy region (86,009 bp), a small single-copy region (18,153 bp), and two inverted repeat regions (28,597 bp). A total of 35 SSR markers were found in the chloroplast genome of Nephelium lappaceum, of which 33 were monomer, 1 was dimer and 1 was tetramer. Phylogenetic analysis based on the complete chloroplast genome sequences of 21 plant species showed that rambutan was closely related to Pometia tomentosa. These results provide a foundation for further phylogenetic and evolutionary studies of the Sapindaceae family.

The complete chloroplast genome of Passiflora caerulea, a tropical fruit with a distinctive aroma.

Passiflora caerulea is native to brazil. In recent years, the edible, medicinal, and ornamental value of P. caerulea has stimulated its wide cultivation in Southeast Asian countries, especially China. Because the chloroplast genome is rich with information about the species evolution as well as its genetic relationship to other species, the P. caerulea chloroplast genome was sequenced, assembled, and annotated in this study. The P. caerulea chloroplast genome is 151,362 bp in total with an overall GC content of 37.03%. It has a quadripartite structure, includes a large single-copy region (LSC, 85,623 bp), a small single-copy region (SSC, 13,397 bp), and two inverted repeat regions (IRa and IRb, 26,180 bp combined). There are 131 genes in the P. caerulea chloroplast genome, including 79 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 7 pseudogenes. Phylogenetic analysis of 29 Passiflora spp. showed that P. caerulea is most closely related to P. edulis. These results provide a considerable foundation for P. caerulea conservation genetics research.

The complete chloroplast genome of Morinda citrifolia (noni).

Morinda citrifolia L. (Rubiaceae), commonly called noni, is a medicinal plant that is often used as botanical dietary supplement. This study is the first to report and characterize the complete chloroplast genome of M. citrifolia. We found that it contains 153,113 bp with a GC content of 38.05%, consisting of two inverted repeat regions (IRs, 25,588 bp), a large single-copy region (LSC, 83,974 bp), and a small single copy (SSC, 17,963 bp) region. One hundred and twenty-five genes were annotated, including 84 protein-coding genes, 33 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that M. citrifolia and Gynochthodes officinalis were closely related. Overall, this study provided a wealth of information for a follow-up phylogenetic and evolutionary study of the Gentianales.

The complete chloroplast genome of Hevea camargoana.

Hevea camargoana is a natural latex producing tropical plant and a close relative of H. brasiliensis, the primary commercial source of natural rubber. This study sequenced and analyzed the chloroplast genome of H. camargoana. The circular chloroplast genome of H. camargoana contains 161,291 bp with a GC content of 35.72%. This region contains two inverted repeat regions (26,819 bp), a large single-copy region (89,281 bp), and a small single-copy (18,372 bp) region in the complete chloroplast genome. A total of 134 genes were annotated, including 86 protein-coding genes, 36 transfer RNA genes, 8 ribosomal RNA genes, and 4 pseudogenes. The results showed that H. camargoana and H. brasiliensis were closely related, suggesting that H. camargoana may be used for the future variety improvement of rubber trees.

Complete chloroplast genome of Hevea benthamiana, a SALB-resistant relative wild species of rubber tree.

Hevea benthamiana is a SALB-resistant wild species of H. brasiliensis, the only source of mass production of high quality natural rubber. This study sequenced and analyzed the chloroplast genome of H. benthamiana. The chloroplast genome of H. benthamiana contains 161,124 bp and consists of 51,495 bp of A (31.96%), 52,022 bp of T (32.29%), 28,915 bp of G (17.95%), and 28,692 bp of C (17.81%). The ring-shaped genome includes four regions: a large single-copy region (LSC, 89,110 bp), a small single copy (SSC, 18,376 bp) region, and two inverted repeat regions (IRs, 26,819 bp). A total of 134 genes were annotated, of which 86 encode proteins; four are pseudogenes; 36 are tRNA genes, and eight are rRNA genes. Phylogenetic analyses showed that H. benthamiana is very closely related to H. Brasiliensis, this result indicates that H. benthamiana is highly valuable for the breeding of SALB-resistant varieties of rubber trees.

Complete chloroplast genome of Synsepalum dulcificum D.: a magical plant that modifies sour flavors to sweet.

Synsepalum dulcificum D. belongs to the Sapotaceae family, which is an evergreen shrub native to tropical West Africa. It is a kind of magical plant that has the unique characteristic of modifying sour flavors to sweet. In this study, the chloroplast genome of S. dulcificum was sequenced, assembled, and annotated firstly. Chloroplast genome size of S. dulcificum is 158,463 bp, the circular chloroplast genome consists of four regions: a large single-copy region of 88,256 bp, two inverted repeat regions of 25,958 bp, and a small single-copy region of 18,669 bp, with the GC content of 36.87%. A total of 133 genes were annotated in the S. dulcificum chloroplast genome, of which 88 were protein-coding genes (PCGs), 37 were transfer RNA (tRNA) genes, and eight were ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that Pouteria campechiana was most closely related to S. dulcificum. The study provides important genomic data for further utilization and breeding of S. dulcificum.

The complete chloroplast genome of Annona muricata L.: a tropical fruit with important medicinal properties.

Annona muricata L. (A. muricata) is an important tropical fruit and medicinal plant. It is one of the easily found plants used traditionally in treating cancer. In many tropical countries, especially in Southeast Asia, A. muricata is popular for its edible fruit and medicinal merits. In this study, the complete chloroplast genome of A. muricata was sequenced, assembled, and annotated. The chloroplast genome of A. muricata was found to be a double strand ring structure with the size of 196,038 bp that consists of four regions: a large single-copy region of 75,339 bp, a small single-copy region of 3105 bp, and two inverted repeat regions of 58,797 bp. The GC content of the whole chloroplast genome was 39.92%. It was found that 111 protein-coding genes, one Pseudogene, 38 tRNA genes, and eight rRNA genes were annotated in the chloroplast genome, and the total number of genes was 158. DNA sequences of the chloroplast genomes of 19 species which belonged to three families of Magnoliales order were analyzed and a phylogenetic tree was constructed. The result indicated that A. muricata, Annona cherimola, Uvaria macrophylla, Greenwayodendron suaveolens, and Chieniodendron hainanense had a close phylogenetic relationship. The findings also provided abundant basic data for the genomics study of A. muricata.

Complete chloroplast genome sequence and phylogenetic analysis of Annona reticulata.

Annona reticulata is native to South and Central America which has many phytochemical and pharmacological activities suggesting a wide range of clinical application in lieu of cancer chemotherapy. This study provides abundant genomic data for the genetic relationship study, germplasm resources evaluation and varieties selection of A. reticulata. The complete chloroplast genome of A. reticulata was sequenced, assembled, and annotated in this study. The genome size was 201,906 bp and was divided into four regions: a large single-copy region of 69,650 bp, a small single-copy region of 3,014 bp, and two inverted repeat regions of 64,621 bp. A total number of 164 genes were annotated, including 115 protein-coding genes, one pseudogene, 40 tRNA genes, and eight rRNA genes. In terms of gene function, the 164 genes were divided into four major groups: genes for self-replication, photosynthesis, unknown function, and other genes. A maximum likelihood tree based on the chloroplast genome sequences of 24 plant species was constructed. The result of phylogenetic analysis showed that A. cherimola had the closest relationship with A. reticulate.

The complete chloroplast genome sequence of Manilkara zapota (Linn.) van Royen.

The complete chloroplast genome sequences of Manilkara zapota (Linn.) van Royen in Xishuangbanna, Yunnan province were reported in this study. The length of the sequence was 159,853 bp long with the large single copy (LSC) region of 89,632 bp, the small single copy (SSC) region of 18,747 bp, and two inverted repeat (IR) regions of 27,737 bp. The plastome contained 125 genes, including 84 protein-coding, 8 ribosomal RNA, and 33 transfer RNA genes. The overall GC content was 37.0%. Phylogenetic analysis of 12 representative plastomes within the order Ebenales suggests that M. zapota (Linn.) van Royen is closely related to the species in family Ebenaceae.

The complete chloroplast genome of Theobroma grandiflorum, an important tropical crop.

Theobroma grandiflorum (Willd. ex Spreng.) K. Schum., an economically important tree in the family Malvaceae, is native to the Amazonian region of South America and it is widely cultivated as a tropical crop. Herein, we report the complete chloroplast genome of T. grandiflorum. The size of the complete chloroplast genome of T. grandiflorum is 160,606 bp with 36.88% GC content, which includes a pair of inverted repeat regions (IRs) of 25,496 bp separated by a large single-copy region (LSC) of 89,429 bp and a small single copy (SSC) region of 20,185 bp. A total of 126 genes were annotated, of which 82 were protein-coding genes, 36 were transfer RNA (tRNA) genes, and 8 were ribosomal RNA (rRNA) genes. A maximum-likelihood (ML) analysis supported a close relationship between T. grandiflorum and T. cacao. This study will provide useful information for further phylogenetic and evolutionary analysis of Malvaceae.

Complete chloroplast genome of Helicia nilagirica Bedd. and its phylogenetic analysis.

Helicia nilagirica Bedd. is a medicinal plant. Its fruit is the main raw material from which helicid, a compound that has sedative, hypnotic, analgesic, and other central nervous system inhibitory effects, is extracted. Here, we report and characterize the complete chloroplast genome of H. nilagirica in this study. The complete chloroplast genome of H. nilagirica contains 157,217 bp and consists of four regions, including a large single-copy region (LSC, 85,516 bp), two inverted repeat regions (IRs, 26,700 bp), and a small single copy (SSC, 18,301 bp) region. A total of 132 genes were obtained by annotation, including 88 protein-coding genes, 36 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that H. nilagirica is closely related to Macadamia integrifolia, suggesting that H. nilagirica may be used as rootstock or gene donor in macadamia breeding. This study lays a foundation for future phylogenetic and evolutionary studies of Proteaceae.

Chloroplast genome of tropical and sub-tropical fruit tree Clausena lansium (Rutaceae).

The Clausena lansium, originally native to the southern part of China and has a long history of cultivation, is a tree member of the family Rutaceae. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of C. lansium for the first time (accession number of MH047377). The chloroplast genome is 159,284 bp long and includes 113 genes. It's LSC, SSC, and IR regions are 88,634, 18,896, and 25,877 bp long, respectively. Phylogenetic tree analysis exhibited that C. lansium was clustered with other Rutaceae species with high bootstrap values.

Chloroplast genome of tropical and sub-tropical fruit tree Syzygium samarangense (Myrtaceae).

Syzygium samarangense is an important fruit of Myrtaceae family and commercially planted in tropical areas of the world. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of S. samarangense for the first time (accession number of MH371141). The chloroplast genome is 159,109 bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,533, 18,882, and 25,847 bp long, respectively. Phylogenetic tree analysis exhibited that S. samarangense was clustered with other Myrtaceae species with 100% bootstrap values.

The complete chloroplast genome sequence of flowering banana, Musa ornata.

Musa ornata (flowering banana) is one of more than 50 species of banana in the genus Musa of the family Musaceae. As sources of resistance to pathogens exist in germplasm, M. ornata is one of the possible hybrid parents for ameliorate commercial banana varieties. Herein, we report the complete chloroplast genome of M. ornata. The total length of the chloroplast genome is 169,989 bp with 36.82% GC content. The genome consisted of 35,426 bp of a pair of inverted repeat regions (IRs), 10,775 bp of small single copy region (SSC) and 88,362 bp of large single-copy region (LSC). A total of 136 functional genes were annotated, including 113 unique genes comprising 79 protein-coding genes, 4 ribosomal RNA (rRNA) genes and 30 transfer RNA (tRNA) genes. Maximum-likelihood phylogenetic analysis with Musaceae and Zingiberaceae species revealed that M. ornata is most closely grouped with Musa acuminata.

The whole chloroplast genome sequence of Macadamia tetraphylla (Proteaceae).

Macadamia tetraphylla (Proteaceae) is one of the two macadamia plants that are edible and of cultivated value. Only two chloroplast genomes were reported in Proteaceae so far. In this study, we report the complete chloroplast genome sequence of M. tetraphylla, which is the third reported chloroplast genome in Proteaceae. The chloroplast genome is 159,195 bp long and includes 113 genes. Its LSC, SSC and IR regions are 87,951, 18,748 and 26,248 bp long, respectively. Phylogenetic analysis indicates that M. tetraphylla was clustered with other two species of Proteaceae, the M. integrifoia and M. ternifolia.

The complete chloroplast genome of tropical and sub-tropical fruit tree Lucuma nervosa (Sapotaceae).

The Lucuma nervosa, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Sapotaceae). Chloroplast genome sequences play an significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of L. nervosa for the first time. The chloroplast genome is 157,920 bp long and includes 113 genes. Its LSC, SSC, and IR regions are 88,123, 18,861, and 25,468 bp long, respectively. Phylogenetic tree analysis exhibited that L. nervosa was clustered with other Sapotaceae species with high bootstrap values.