The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations.

MAIN CONCLUSION: The first complete mitochondrial genome of Carex (C. breviculmis) was sequenced and assembled, and its genomic signature was analyzed and the possible conformations of its mitochondrial genome were validated. Carex breviculmis is a very adaptable grass that is highly resistant to environmental stresses such as drought and low light. It is also admired as a landscape plant with high development prospects and scientific research value. In this study, the mitochondrial genome of C. breviculmis was assembled using Pacbio and Illumina sequencing data. We detected 267 pairs of repeats and found that three pairs of repeats could mediate the recombination of its mitochondrial genome and formed four possible conformations, of which we verified the two conformations mediated by the shortest pair of repeats using PCR amplification and Sanger sequencing. The major conformation of the C. breviculmis mitochondrial genome is a 1,414,795 bp long circular molecule with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected a total of 25 homologous sequences between the chloroplast and mitochondrial genomes, corresponding to 0.40% of the mitochondrial genome. Combined with the low GC content (41.24%), we conclude that the reduction in RNA editing sites in the C. breviculmis mitochondrial genome may be due to an accumulation of point mutations in C-to-T or retroprocessing events within the genome. The relatively low number of RNA editing sites in its mitochondrial genome could serve as important material for subsequent studies on the selection pressure of RNA editing in angiosperms. A maximum likelihood analysis based on 23 conserved mitochondrial genes from 28 species reflects an accurate evolutionary and taxonomic position of C. breviculmis. This research provided us with a comprehensive understanding of the mitochondrial genome of Carex and also provided important information for its molecular breeding.

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure.

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

[Genetic diagnosis of a Chinese pedigree affected with Alazami syndrome].

OBJECTIVE: To explore the genetic etiology for a Chinese pedigree affected with Alazami syndrome. METHODS: Genomic DNA was extracted for 2 patients and 2 unaffected members from the pedigree. Whole exome sequencing was carried out to detect potential variant in the proband, and the result was verified by Sanger sequencing. RESULTS: The proband and her sister were both found to harbor compound heterozygous variants of LARP7 gene, namely c.94A>T (p.Lys32*) and c.1141A>G (p.Lys381Glu), which were inherited from their father and mother, respectively. Both variants were predicted to be pathogenic based on bioinformatic analysis. CONCLUSION: The two variants of the LARP7 gene, both were unreported previously, probably underlay the Alazami syndrome in this pedigree. Above finding has expanded the mutational spectrum of the LARP7 gene.

Phylogenomics and Biogeography of Populus Based on Comprehensive Sampling Reveal Deep-Level Relationships and Multiple Intercontinental Dispersals.

Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus, and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA-BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus. The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso. Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus.

The complete chloroplast genome sequence of Dianyuea turbinata (H.J. Dong & H. Peng) C. Shang, S. Liao & Z.X. Zhang (Salicaceae).

The chloroplast genome sequences of Dianyuea turbinata (H.J. Dong & H. Peng) C. Shang, S. Liao & Z.X. Zhang, endemic to Yingjiang County, Yunnan Province, China, was presented in this study (Dong and Peng 2013; Shang et al. 2017). The chloroplast genome sequence was 154,045 bp in length, with a large single-copy (LSC) region of 82,247 bp, a small single-copy (SSC) region of 16,522 bp, separated by two inverted repeat (IR) regions of 27,638 bp each. The total GC content was 37.1%. The complete plastome sequence contained 134 genes, including 89 protein-coding, 37 tRNA and 8 rRNA genes. The phylogenetic status of genus Dianyuea has been clarified through a Maximum-likelihood tree based on the chloroplast genome of 17 species.

The complete chloroplast genome of Cratoxylum cochinchinense (Hypericaceae).

Cratoxylum cochinchinense (Lour.) Blume is a tropical Asia specie limited distributed from South China to Borneo. The complete chloroplast genome of the species was found to be 157,103 bp in length, with 129 unique genes, including 37 tRNA, eight rRNA, and 84 protein-coding genes. The GC content of C. cochinchinense is 36.2%. As the first complete chloroplast genome in Hypericaceae, it shows the phylogenetic relationship within Malphigiales.

Development, structure and evolutionary significance of seed appendages in Salix matsudana (Salicaceae).

The seeds of Salix and Populus (Salicaceae) are characterized by having numerous long hairs which loosely accompanying the seeds and a small annular appendage which surrounding the base of the seed along with tufted hairs. In this study, the complete development and detailed structure of the hairs and annular appendage in Salix matsudana were investigated using standard techniques for plant anatomy and histochemistry. The results show that the hairs originate successively from the single epidermal cells of the placenta (in megaspore mother cell phase) and funiculus (in eight-nucleate phase), and that their development consists of a progressive increase in cell size and an absence of cell division. The annular appendage is initiated from four to five rows of cells at the distal end of the funiculus in octant proembryo phase and its development is characterized by reactivated meristematic activity and a size increase of these cells. The initiation and development of the hairs are irrelevant to ovule development but fertilization and a developed embryo is necessary for the annular appendage to occur. Considering the reliable fossils, we inferred that the feature of seeds surrounded by long hairs is an ancestral character, and that the detachment of hairs from the funiculus and the occurrence of an annular appendage with tufts of hairs may be the more derived states for seed dispersal in Salix and Populus.