Xinyi Guo

Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

Genetic variations from few chloroplast DNA fragments show lower discriminatory power in the delimitation of closely related species and less resolution ability in discerning interspecific relationships than from nrITS. Here we use Orychophragmus (Brassicaceae) as a model system to test the hypothesis that the whole chloroplast genomes (plastomes), with accumulation of more variations despite the slow evolution, can overcome these weaknesses. We used Illumina sequencing technology via a reference-guided assembly to construct complete plastomes of 17 individuals from six putatively assumed species in the genus. All plastomes are highly conserved in genome structure, gene order, and orientation, and they are around 153 kb in length and contain 113 unique genes. However, nucleotide variations are quite substantial to support the delimitation of all sampled species and to resolve interspecific relationships with high statistical supports. As expected, the estimated divergences between major clades and species are lower than those estimated from nrITS probably due to the slow substitution rate of the plastomes. However, the plastome and nrITS phylogenies were contradictory in the placements of most species, thus suggesting that these species may have experienced complex non-bifurcating evolutions with incomplete lineage sorting and/or hybrid introgressions. Overall, our case study highlights the importance of using plastomes to examine species boundaries and establish an independent phylogeny to infer the speciation history of plants.

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.

Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long‐distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E. salsugineum. Our population genomic data indicate that E. salsugineum migrated “out of the Altai region” at least three times to colonize northern China, northeast Russia and western China. It then expanded its distribution into North America independently from northeast Russia and northern China, respectively. The species colonized northern China around 33.7 thousand years ago (kya) and underwent a considerable expansion in range size approximately 7–8 kya. The western China lineage is likely a hybrid derivative of the northern China and Altai lineages, originating approximately 25–30 kya. Deleterious alleles accumulated in a stepwise manner from (a) Altai to northern China and North America and (b) Altai to northeast Russia and North America. In summary, E. salsugineum dispersed from Asia to North America and deleterious mutations accumulated in a stepwise manner during the expansion of the species’ distribution.

Characterization of the complete chloroplast genome of Musella lasiocarpa

Abstract The whole chloroplast (cp) genome sequence of Musella lasiocarpa has been characterized from Illumina pair-end sequencing. The complete cp genome was 169,178 bp in length, containing a large single copy (LSC) region of 87,884 bp and a small single copy (SSC) region of 11,144 bp, which were separated by a pair of 35,075 bp inverted repeat (IR) regions. The genome contained 138 genes, including 88 protein-coding genes (87 PCG species), 37 tRNA genes (30 tRNA species), and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 23 gene species occur in double copies. The overall AT content of M. lasiocarpa cp genome is 63.3%, while the corresponding values of the LSC, SSC, and IR regions are 64.9, 69.2, and 60.3%, respectively. The cp genome sequence is similar to that of the genus Musa.

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Abstract Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well‐resolved phylogeny from the perspective of the plastomes.

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.