Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis.

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

The complete chloroplast genome sequence of Camellia chuongtsoensis.

Camellia chuongtsoensis is an evergreen shrub with a single-petaled flower and golden yellow color. The complete chloroplast genome of C. chuongtsoensis was sequenced and analyzed in this study by Illumina sequencing. The chloroplast genome is 156,504 bp in length with a quadripartite structure containing a large single copy (LSC) region of 86,215 bp, a small single copy (SSC) region of 18,253 bp, and a pair of inverted repeat regions of 26,018 bp (IRa and IRb). The chloroplast genome of C. chuongtsoensis encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes.

Complete chloroplast genome sequence of Camellia rhytidophylla, comparative and phylogenetic analysis.

Camellia rhytidophylla is an endangered plant with economic value. Using Illumina sequencing, the chloroplast genome of C. rhytidophylla was sequenced and analyzed in this study. The complete chloroplast genome is 157,073 bp in length, which consisted of a pair of inverted repeat regions of 26,055 bp (IRa and IRb) separated by a large single-copy region (LSC) of 86,680 bp and a small single-copy region (SSC) of 18,283 bp. The C. rhytidophylla chloroplast genome encodes 135 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes. Sequence comparison analysis with the chloroplast sequences of 28 other Camellia plants found that C. rhytidophylla had the closest relationship with C. szechuanensis. This study provides a theoretical basis for the analysis of the distant relationship of Camellia.

Complete chloroplast genome sequence and phylogenetic analysis of Camellia fraterna.

Camellia fraterna belongs to the genus Camellia in the family Theaceae. We sequenced and analyzed the complete chloroplast genome of C. fraterna by Illumina sequencing in this study. The full length of the complete chloroplast genome is 156,902 bp, containing a pair of inverted repeat regions of 26,030 bp (IRa and IRb) separated by a large single-copy (LSC) region of 86,583 bp and a small single-copy (SSC) region of 18,259 bp. The C. fraterna chloroplast genome encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and three pseudogenes. This study will be useful for further study on genetic diversity and molecular breeding.

Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma longa (Zingiberaceae).

Curcuma longa, a well-known traditional medicinal plant in China, belongs to the genus Curcuma family Zingiberaceae. In this study, we firstly assembled the complete chloroplast genome of C. longa based on sequences from Illumina and PacBio sequencing platforms. We obtained the complete chloroplast genome with the total length of 162,176 bp. It consisted of a large single-copy region (LSC, 86,984 bp), a small single-copy region (SSC, 15,694 bp), and a pair of inverted repeats (IRs, 29,749 bp each). Sequence analyses indicated that the chloroplast genome contained 111 distinct genes including 79 protein-coding genes, 28 tRNA genes, and four rRNA genes. The nucleotide composition was asymmetric (31.62% A, 18.42% C, 17.79% G, 32.18% T) with an overall AT content of 63.80%. The AT contents of the LSC, SSC and IR regions were 66.00%, 70.35% and 58.85%, respectively. Sixteen genes owned a single intron, while another two genes had two introns. The phylogenetic analysis indicated that C. longa was closely related to species Curcuma roscoeana within the genus Curcuma in family Zingiberaceae.

Complete chloroplast genome sequence of Amomum villosum.

The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.

Complete chloroplast genome sequence of Hedychium coronarium.

The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.

[Effects of different landscape patch structure on the diversity of arthropod community in tea plantations].

A field survey with random block design was conducted to study the effects of different landscape patch structure on the arthropod community in tea plantations. In the tea plantations with small woodland (QM) or Acacia confuse (XS) patches, predatory spider had the highest proportion, occupying 62.3% and 69.5% of the total arthropods, respectively, being significantly higher than that in the tea plantations close to paddy field (DT) or near a village (RJ). The tea plantations with QM had the highest diversity index and species richness of arthropod community, while the evenness index and dominance index were not significantly different from the other tea plantations. The tea plantations with QM and XS had much richer natural enemies, and the order of the diversity index, evenness index, and richness index of natural enemies in the tea plantations ranked as QM > XS > DT > RJ. It was suggested that landscape patch structure had great effect on the diversity of arthropod community in tea plantations.