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The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum (Fagopyrum) tibeticum. Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum (Fagopyrum) tibeticum, Atraphaxis bracteata and Calligonum ebinuricum. Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum (Fagopyrum) tibeticum, A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum. Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum, which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.

Populations of widespread species are usually geographically distributed through contrasting stresses, but underlying genetic mechanisms controlling this adaptation remain largely unknown. Here, we show that in Arabidopsis thaliana , allelic changes in the cis-regulatory elements, WT box and W box, in the promoter of a key transcription factor associated with oxygen sensing, RELATED TO AP 2.12 (RAP2.12), are responsible for differentially regulating tolerance to drought and flooding. These two cis-elements are regulated by different transcription factors that downstream of RAP2.12 results in differential accumulation of hypoxia-responsive transcripts. The evolution from one cis-element haplotype to the other is associated with the colonization of humid environments from arid habitats. This gene thus promotes both drought and flooding adaptation via an adaptive mechanism that diversifies its regulation through noncoding alleles.

Populations of widespread species are usually geographically distributed through contrasting stresses, but underlying genetic mechanisms controlling this adaptation remain largely unknown. Here, we show that in

Toona sinensis is an economic and medicinal plant endemic in China. In this study, the complete chloroplast genome of T. sinensis was assembled using the second-generation high-throughput sequencing data. The genome consists of 138 genes in total, including 89 protein-coding genes, 7 ribosomal RNA genes, 40 transfer RNA genes and 2 pseudogenes. Phylogenetic analysis indicated that T. sinensis has a close relationship with the Toona ciliata with strong support. The chloroplast genome presented here provides a valuable resource to conserve this valuable species.

Nannoglottis ravida is an extremely endangered species in the Qinghai-Tibet Plateau. Based on the second-generation high-throughput genome sequencing, we assembled the plastome of this species. The length of the total plastome is 152,324 bp with a typical quadripartite structure including a large single-copy region of 83,708 bp, a small single-copy region of 29,882 bp and two reverse repeat regions of 19,367 bp respectively. A total of 131 genes were annotated including 85 protein-coding genes (PCG), 36 tRNA genes, 8 rRNA genes and 2 pseudogenes. The constructed phylogenetic tree with other species of two tribes Senecioneae and Astereae based on plastomes suggests that N. ravida has a close relationship with the Astereae, but diverged early from this tribe.

Davidia involucrata Baill, also known as the dove-tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome-scale genome of this species using single-molecule real-time long reads and chromosome conformation capture (Hi-C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove-tree. Photosynthesis-related genes were almost absent or showed reduced expression in the bracts of the dove-tree, while defence- and chemical-related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove-tree continuously decreased during the climate changes of the Quaternary. Such climate sensitivity should be fully considered in conservation efforts for this relict endangered species in the context of continuous climate warming in the future.

Toona sinensis is an economic and medicinal plant endemic in China. In this study, the complete chloroplast genome of T. sinensis was assembled using the second-generation high-throughput sequencing data. The genome consists of 138 genes in total, including 89 protein-coding genes, 7 ribosomal RNA genes, 40 transfer RNA genes and 2 pseudogenes. Phylogenetic analysis indicated that T. sinensis has a close relationship with the Toona ciliata with strong support. The chloroplast genome presented here provides a valuable resource to conserve this valuable species.

Torreya parvifolia (Torreya, Taxaceae) is endemic in Sichuan, China. It consisted of an extremely small population with less than 100 wild individuals. In this study, the complete chloroplast genome of T. parvifolia was assembled using the Illumina data. The complete chloroplast genome of T. parvifolia is 137,106 bp in length. The genome consists of 119 genes in total, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. Phylogenetic analysis indicated that T. parvifolia was closely related to T. fargesii, T. nucifera, and T. fargesii var. yunnanensis with strong support.

The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum (Fagopyrum) tibeticum. Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum (Fagopyrum) tibeticum, Atraphaxis bracteata and Calligonum ebinuricum. Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum (Fagopyrum) tibeticum, A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum. Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum, which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum., Highlights • We resolved the previously controversial phylogenetic position of genus Parapteropyrum. • Our plastome assembly and phylogeny reconstruction are robust to various reference sequences. • Our study first reported plastome data for all the genera of the Trib. Atraphaxideae Damm.

Torreya parvifolia (Torreya, Taxaceae) is endemic in Sichuan, China. It consisted of an extremely small population with less than 100 wild individuals. In this study, the complete chloroplast genome of T. parvifolia was assembled using the Illumina data. The complete chloroplast genome of T. parvifolia is 137,106 bp in length. The genome consists of 119 genes in total, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. Phylogenetic analysis indicated that T. parvifolia was closely related to T. fargesii, T. nucifera, and T. fargesii var. yunnanensis with strong support.

Cupressus jiangeensis is a critically endangered conifer listed in the IUCN Red List of Threatened Species. Illumina pair-end reads of this species was used to character the whole chloroplast (cp) genome sequence. The circular genome with 128,286 bp in length contains two duplicated genes (trnL and trnQ) and 115 single copy genes, including 82 protein-coding genes, 31 tRNA and four ribosomal RNA genes. Eight genes (atpF, ndhA, ndhB, rpoC1, petD, petB, rpl16 and rpl2) have a single intron, while two genes (rps12 and ycf3) have two introns. There are no inverted repeat sequences in this genome. The GC content of this cp genome is 34.68%. Phylogenomic analysis strongly supported the close relationship of C. jiangeensis and C. chengiana.

Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.

Antiaris toxicaria (Antiaris, Moraceae) is a medicinal and extremely toxic species. To facilitate species identification and provide genetic information, we determined the complete chloroplast genome of A. toxicaria using the Illumina platform. The genome was 161,412 bp in length, comprising a large single-copy region (LSC) of 89,883 bp, a small single-copy region (SSC) of 20,375 bp, and a pair of inverted repeats (IRs) of 25,577 bp each. The genome contained 130 encoded genes in total, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the A. toxicaria chloroplast genome is 35.87%. The phylogenetic analysis revealed A. toxicaria was closely related to the genus Ficus within the family Moraceae.