Hua-Feng Wang

Variation of Soil Bacterial Communities in a Chronosequence of Rubber Tree (Hevea brasiliensis) Plantations

Regarding rubber tree plantations, researchers lack a basic understanding of soil microbial communities; specifically, little is known about whether or not soil microbial variation is correlated with succession in these plantations. In this paper, we used high-throughput sequencing of the 16S rRNA gene to investigate the diversity and composition of the soil bacterial communities in a chronosequence of rubber tree plantations that were 5, 10, 13, 18, 25, and 30 years old. We determined that: (1) Soil bacterial diversity and composition show changes over the succession stages of rubber tree plantations. The diversity of soil bacteria were highest in 10, 13, and 18 year-old rubber tree plantations, followed by 30 year-old rubber tree plantations, whereas 5 and 25 year-old rubber tree plantations had the lowest values for diversity. A total of 438,870 16S rDNA sequences were detected in 18 soil samples from six rubber tree plantations, found in 28 phyla, 66 classes, 139 orders, 245 families, 355 genera, and 645 species, with 1.01% sequences from unclassified bacteria. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Verrucomicrobia (relative abundance large than 3%). There were differences in soil bacterial communities among different succession stages of rubber tree plantation. (2) Soil bacteria diversity and composition in the different stages was closely related to pH, vegetation, soil nutrient, and altitude, of which pH, and vegetation were the main drivers.

Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered “Vulnerable” in Southeast Asia

Abstract Dracaena cambodiana (Asparagaceae) is a treelike plant ranging from 3 to 10 m tall. It grows in low-elevation forests (0–300 m) having dry and sandy soils. It is distributed in Southern Hainan Island in China and other Southeast Asian countries (e.g. Cambodia, Laos, Thailand and Vietnam). The dried resin can be used medicinally as a substitute for that of Dracaena cochinchinensis. It has been ranked as a Vulnerable (VU) species in China. Here we report and characterize the complete plastid genome sequence of D. cambodiana. The complete plastome is 156,697 bp in length. It contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,526 bp, a Large Single-Copy (LSC) region of 84,988 bp and a Small Single-Copy (SSC) region of 18,657 bp. The plastome contains 113 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes and three pseudogenes (i.e. matK, infA, ndhF). The overall A/T content in the plastome of D. cambodiana is 62.4%. We performed phylogenetic analyses using the entire plastome, including spacers, introns, etc., and we determined that D. cambodiana and Maianthemum bicolor were closely related. The complete plastome sequence of D. cambodiana will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Asparagales.

Complete plastome sequence of Vatica mangachapoi (Dipterocarpaceae): a vulnerable (VU) plant species in Southeast Asia

Abstract Vatica mangachapoi is a tree up to 20 m tall with white resinous. It is distributed in China (Hainan province), Indonesia, Malaysia (N Borneo), Philippines, Thailand, and Vietnam. It grows in forests on hills and mountain slopes below 700 metres. Its durable wood is used for making boats and building bridges and houses. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of V. mangachapoi in an effort to provide genomic resources useful for promoting its conservation and phylogenetic research. The complete plastome is 151,538 bp in length and contains the typical structure and gene content of angiosperm plastome, including two Inverted Repeat (IR) regions of 23,921 bp, a Large Single-Copy (LSC) region of 83,587 bp and a Small Single-Copy (SSC) region of 20,109 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and 4 unique rRNA genes. The overall A/T content in the plastome of V. mangachapoi is 62.80%. The phylogenetic analysis indicated that V. mangachapoi and V. odorata is closely related and as an independent branch in Malvales in our study. The complete plastome sequence of V. mangachapoi will provide a useful resource for the conservation genetics of this species and for the phylogenetic studies for Vatica.

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China

Abstract Scurrula notothixoides (Loranthaceae) is a hemiparasitic shrub distributed in forest margins of Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. notothixoides in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete plastome is 123,810 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 23,101 bp, a large single copy (LSC) region of 71,448 bp and a small single copy (SSC) region of 6160 bp. The plastome contains 88 genes, consisting of 61 unique protein-coding genes, 23 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of S. notothixoides is 62.7%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc. and we recovered that S. notothixoides and Taxillus sutchuenensis was closely related. The complete plastome sequence of S. notothixoides will provide a useful resource for the phylogenetic studies for Santalales.

Complete plastome sequence of Piper laetispicum (Piperaceae): An endemic plant species in South China

Abstract Piper laetispicum is dioecious climbers woody with 10 m tall, which is an endemic species in China. It grows on trees or rocks in forests (100–600 m) in Guangdong and Hainan Province of China. Here, we report and characterize the complete plastid genome sequence of P. laetispicum in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 161,721 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,125 bp, a large single copy (LSC) region of 89,224 bp and a small single copy (SSC) region of 18,247 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and four unique rRNA genes. The overall A/T content in the plastome of P. laetispicum is 61.70%. The complete plastome sequence of P. laetispicum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Piper.

Complete plastome sequence of Nepenthes mirabilis (Nepenthaceae): a “vulnerable” herb in China

Abstract Nepenthes mirabilis (Nepenthaceae) is an erect or climbing (0.5–2 m tall) herb distributed in Africa (Madagascar), south and southeast Asia, North Australia and Pacific Islands (Caroline Islands). There is only one species in China. It grows in wet and sandy soils places throughout forests, grasslands, swamps, mountains, roadsides, wastelands having altitudes that sea level to 400 m. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of N. mirabilis in an effort to provide genomic resources useful for its conservation. The complete plastome is 155,755 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,415 bp, a Large Single-Copy (LSC) region of 84,997 bp and a Small Single-Copy (SSC) region of 17,928 bp. The plastome contains 113 genes, consisting of 77 unique protein-coding genes, three pseudogenes, 29 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of N. mirabilis is 62.8%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc., and we determined that N. mirabilis 32 and Dionaea muscipula were closely related. The complete plastome sequence of N. 33 mirabilis will provide a useful resource for the conservation genetics of this species as 34 well as for the phylogenetic studies in Caryophyllales.

Complete plastome sequence of Hydnocarpus hainanensis Merr (Achariaceae): an endemic ‘vulnerable’ tree in South China

Abstract Hydnocarpus hainanensis Merr. is an evergreen tree with a height of 6–12 m and a diameter at breast height of 50 cm. It is distributed in Guangxi, Guizhou, Hainan, South of Yunnan Province of China. Here, we report and characterize the complete plastid genome sequence of H. hainanensis in an effort to provide genomic resources useful for promoting its conservation and systematics research. The plastome of H. hainanensis is found to possess a total length 163,330 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 26,870 bp, a large single copy (LSC) region of 91,510 bp and a small single copy (SSC) region of 18,080 bp. The plastome contains 111 genes, consisting of 78 unique protein-coding genes (seven of which are duplicated in the IR: rps12, rps7, ndhB, ycf2, rpl23, rpl2, and rps19), 29 unique tRNA genes (seven of which are duplicated in the IR, i.e. trnNGUU, trnRACG, trnAUGC, trnlGAU, trnVGAC, trnLCAA, and trnlCAU) and four unique rRNA genes (5S rRNA, 4.55S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of H. hainanensis is 63.70%. The phylogenetic analysis indicated that H. hainanensis is close to Salix rorida within Malpighiales. The complete plastome sequence of H. hainanensis will provide a useful resource for the conservation genetics of the one species as well as for the phylogenetic studies of Achariaceae.

Complete plastome sequence of Hoya pottsii Traill and Hoya liangii Tsiang (Apocynaceae)

Abstract Hoya is the largest genus (about 350–450 species) within Apocynaceae. It is a subshrub or liana, epiphytic or epilithic. Most species grow in tropical and subtropical South and Southeast Asia. Here we report and characterize the complete plastid genome sequence of Hoya pottsii Traill and Hoya liangii Tsiang in an effort to provide genomic resources useful for promoting its systematics research. The complete plastome of H. pottsii is 161,565 bp in length, including two Inverted Repeat (IR) regions of 24,657 bp, a Large Single-Copy (LSC) region of 92,532 bp, and a Small Single-Copy (SSC) region of 19,719 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.40%. The complete plastome of H. liangii is 162,989 bp in length, including two IR regions of 24,841 bp, a LSC region of 93,292 bp, and a SSC region of 20,015 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.30%. The complete plastome sequence of H. pottsii and H. liangii will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Hoya.

Complete chloroplast genome sequence of Heritiera angustata (Malvaceae): an endangered plant species

Abstract Heritiera angustata (Malvaceae) is an evergreen tree distributed in the Chinese provinces of Hainan and Yunnan and in Cambodia. In China, it is listed as ‘Endangered’ (EN) China Red List of Higher Plants, although it is not protected by law. The complete chloroplast (cp) genome sequence of this threatened species is reported in this study, based on high-throughput sequencing (Illumina). The complete cp genome is 168, 953 bp in length, containing a pair of inverted repeat regions (IRs) of 34,491 bp, a large single copy (LSC) region of 89,054 bp, and a small single copy (SSC) region of 10,917 bp. The cp genome contains 129 genes, consisting of 85 protein-coding genes, 36 tRNA genes and eight rRNA genes. The overall AT content in the cp genome of H. angustata is 63.2%. The phylogenetic analyses indicate that there is a close relationship between H. angustata and Firmiana pulcherrima.

Complete plastome sequence of Erythropalum scandens (Erythropalaceae), an edible and medicinally important liana in China

Abstract Erythropalum scandens (Erythropalaceae, Santalales) is a large liana distributed in alluvial and riparian forests of Southeast Asia. Here we report and characterize the complete plastid genome sequence of E. scandens in an effort to provide genomic resources useful for developing its medicinal and edible value. The complete plastome is 156,154 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,394 bp, a large single-copy (LSC) region of 84,799 bp and a small single-copy (SSC) region of 18,567 bp. The plastome contains 112 genes, consisting of 79 unique protein-coding genes, 29 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of E. scandens is 62.01%. Phylogenetic analyses were performed using the entire plastome, including genes, spacers and introns, which recovered E. scandens as sister to remaining Santalales with complete plastome sequences.