Guoqian Hao

Plastome phylogeny and early diversification of Brassicaceae

BackgroundThe family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.ResultsBayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.ConclusionsPlastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

The complete chloroplast genome of salt cress (Eutrema salsugineum)

Abstract The complete chloroplast (cp) sequence of the salt cress (Eutrema salsugineum), a plant well-adapted to salt stress, was presented in this study. The circular molecule is 153,407 bp in length and exhibit a typical quadripartite structure containing an 83,894 bp large single copy (LSC) region, a 17,607 bp small single copy (SSC) region, and the two 25,953 bp inverted repeats (IRs). The salt cress cp genome contains 135 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 40 tRNA genes; 21 of these are located in the inverted repeat region. As expected, phylogenetic analysis support the idea that E. salsugineum is sister to Brassiceae species within the Brassicaceae family.

The complete chloroplast genome of Ostrya rehderiana

Abstract The complete chloroplast sequence of Ostrya rehderiana is 159 347 bp in length, containing 85 protein-coding genes, 8 ribosomal RNA genes, and 31 transfer RNA genes. The circular genome exhibits a typical chloroplast genome structure comprising a large single copy region of 88 552 bp, a small single copy region of 18 941 bp and a pair of inverted repeats of 25 927 bp. The overall GC content of the chloroplast genome is 36.5%. Phylogenetic analysis of O. rehderiana sequence together with 12 complete chloroplast genomes revealed a basal placement of O. rehderiana within the Fagales species.

Eutrema giganteum (Brassicaceae), a new species from Sichuan, southwest China

Abstract Eutrema giganteum (Brassicaceae), a new species from Hengduan Mountains in Sichuan Province, southwest China, is described, and its relationships to the closely related E. yunnanense is discussed based on morphological, cytological, and molecular data. It is similar morphologically to E. yunnanense but is readily distinguished by having robust (vs. slender), erect (vs. decumbent), and branched (vs. mostly simple), and rather tall stems (60–110 cm vs. 20–60 cm); curved (vs. straight), smooth (vs. torulose), and shorter fruit (5–8 mm vs. 8–15 mm); and fewer ovules per ovary (1–4 vs. 6–10). All examined individuals from different populations of E. giganteum clustered into a single clade sister to E. yunnanense in phylogenetic analyses using the combined nuclear ITS and plastid DNA datasets. Our cytological studies revealed that the chromosome number of E. giganteum is 2n = 44, with a genome size of 1160 (±8) Mb, while that of E. yunnanense is 2n = 28, with a genome size of 718 (±15) Mb. Multiple lines of evidence support the recognition of E. giganteum as a distinct species well differentiated from E. yunnanense.

The complete chloroplast genome of Schrenkiella parvula (Brassicaceae).

Abstract Schrenkiella parvula is an Arabidopsis-related model species used here for studying plant stress tolerance. In this study, the complete chloroplast genome sequence of S. parvula has been reported for the first time. The total length of the chloroplast genome was 153 979 bp, which had a typical quadripartite structure. The annotated plastid genome includes 87 protein-coding genes, 39 tRNA genes and 8 ribosomal RNA genes. The evolutionary relationships revealed by our phylogenetic analysis indicated that S. parvula is closer to the Brassiceae species when compared with Eutrema salsugineum.

The whole chloroplast genomes of two Eutrema species (Brassicaceae)

Abstract In this study, we determined the complete chloroplast genomes from two crucifer species of the Eutrema genus. The sizes of the two cp genomes were 153 948 bp (E. yunnanense) and 153 876 bp (E. heterophyllum). Both genomes have the typical quadripartite structure consisting of a large single copy region, a small single copy region and two inverted repeats. Gene contents and their relative positions of the 132 individual genes (87 protein-coding genes, eight rRNA, and 37 tRNA genes) of either genome were identical to each other. Phylogenetic analysis supports the idea that the currently recognized Eutrema genus is monophyletic and that E. salsugineum and Schrenkiella parvula evolved salt tolerance independently.

Phytochemical profiling of five medicinally active constituents across 14 Eutrema species

Wasabi or Japanese horseradish (Eutrema japonicum) is both a traditional condiment and a medicinally important plant with diverse uses. Its medicinally active constituents appear to include five isothiocyanates, but their spatial variations in naturally occurring congeners are unknown. Thus, in this study we measured concentrations of these five active constituents in 20 populations of 14 species of Eutrema and one related species, Yinshania sinuata. Three to five of these constituents were detected in each of the examined species, at concentrations that varied greatly between sampled species and populations of the same species. However, two species, Eutrema tenue and Eutrema deltoideum, had higher total concentrations of the five isothiocyanates and substantially higher concentrations of one or two, than the widely cultivated E. japonicum. Thus, both of these species could be important wild resources for artificial cultivation, in addition to the currently widely cultivated E. japonicum.

The genomes of two Eutrema species provide insight into plant adaptation to high altitudes

Abstract Eutrema is a genus in the Brassicaceae, which includes species of scientific and economic importance. Many Eutrema species are montane and/or alpine species that arose very recently, making them ideal candidates for comparative studies to understand both ecological speciation and high-altitude adaptation in plants. Here we provide de novo whole-genome assemblies for a pair of recently diverged perennials with contrasting altitude preferences, the high-altitude E. heterophyllum from the eastern Qinghai-Tibet Plateau and its lowland congener E. yunnanense. The two assembled genomes are 350 Mb and 412 Mb, respectively, with 29,606 and 28,881 predicted genes. Comparative analysis of the two species revealed contrasting demographic trajectories and evolution of gene families. Gene family expansions shared between E. heterophyllum and other alpine species were identified, including the disease resistance R genes (NBS-LRRs or NLRs). Genes that are duplicated specifically in the high-altitude E. heterophyllum are involved mainly in reproduction, DNA damage repair and cold tolerance. The two Eutrema genomes reported here constitute important genetic resources for diverse studies, including the evolution of the genus Eutrema, of the Brassicaceae as a whole and of alpine plants across the world.