PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics.

The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.

Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm ().

Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae).

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial.

Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae).

Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae.

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica.

Background: Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding".

Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes.

Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species.

Characterization of the complete chloroplast genome of (Poaceae), a widespread weed.

belongs to Poaceae. The complete chloroplast genome of was reported in this study. The chloroplast genome was 137,837 bp in size with a canonical quadripartite structure, including two inverted repeat regions (IR) of 21,635 bp for each, a large single-copy (LSC) region of 81,787 bp in length, and a small single-copy (SSC) region of 12,780 bp in length.

A Novel Alginate Lyase: Identification, Characterization, and Potential Application in Alginate Trisaccharide Preparation.

Alginate oligosaccharides (AOS) have many biological activities and significant applications in prebiotics, nutritional supplements, and plant growth development. Alginate lyases have unique advantages in the preparation of AOS. However, only a limited number of alginate lyases have been so far reported to have potentials in the preparation of AOS with specific degrees of polymerization.

Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Strain GY-D55.

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated.

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae).

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, , , and In this study, the plastomes of and were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types.

Characterization and phylogenetic analysis of the complete plastome of L. (Amaranthaceae), an annual weeds.

The complete plastome of L., a field weed, was identified in this study. The genome size was 150,710 bp and consists of a large single-copy (LSC: 83,892 bp) region, a small single-copy (SSC: 18,100 bp) region, and two inverted repeats (IRs: 24,359 bp) regions.

Characterization and phylogenetic analysis of the complete plastome of (Plantaginaceae).

is a perennial herb, and the complete chloroplast genome (plastome) of was determined in this study. The results showed that the plastome size of was 151,178 bp, including a large single-copy region (68,533 bp), a small single-copy region (21,403 bp), and two inverted repeat regions (25,566 bp). The total GC content of the plastome was 38.

Characterization and phylogenetic analysis of the complete chloroplast genome of (Amaranthaceae).

is an important medicinal herb. In this study, the complete chloroplast genome (plastome) of was repotred. It was a circular molecular of 150,452 bp in length and consists of a large single-copy region (LSC, 83,832 bp), a small single-copy region (SSC, 17,914 bp), and two inverted repeats (IRs, 24,353 bp for each) regions.

Comparative Plastomes and Phylogenetic Analysis of and Closely Related Genera (Poaceae).

(Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of and phylogenetic relationships among taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of , the plastomes of 12 taxa (including 8 species and 4 varieties), one species, 15 species, two species, and two species were included in the present study.

Characterization of the complete plastome of (Asteraceae), a perennial herb.

is a perennial herb that distributes widely in China, Korea, and Eeastern Russia. The complete plastome of is reported here. It is a circular molecular of 152,815 bp in length and consists of a large single-copy region (LSC: 84,530 bp), a small single-copy region (SSC: 18,219 bp), and two inverted repeats (IR: 25,033 bp) regions.

sp. nov. and sp. nov., isolated from marine macroalgae.

Two Gram-stain-negative, aerobic, rod-shaped bacteria, polar flagellated, designated strains SM2066 and SM1966, were respectively isolated from the surfaces of and macroalgae collected off the coastal areas of Rongcheng, PR China. Strain SM2066 grew at 8-37 °C and with 0.5-7.

Characterization of the complete chloroplast genome of (Polygonaceae).

(Polygonaceae) is a fairly common perennial herb of high altitudes. In this study, we determined the complete chloroplast genome (plastome) of with genome-skimming method. The complete plastome of was 159,110 bp in length with a quadripartite structure, including a large single-copy region of 84,810 bp, a small single-copy region of 13,044 bp, and a pair of inverted repeats regions of 30,628 bp.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae).

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed.

Characterization of the complete plastome of (Poaceae), a widespread weed.

is a predominant weed species that distributes widely in North temperate regions. The complete plastome of is reported here. It is a circular molecular of 136,382 bp in length and consists of a large single-copy region (LSC: 80,455 bp), a small single-copy region (SSC: 12,849 bp), and two inverted repeats regions (IRs: 21,539 bp).

Characterization of the complete chloroplast genome of an annual halophyte, (Amaranthaceae).

The complete chloroplast genome (plastome) of , an annual halophytic herb, was determined. The plastome was 152,191 bp in size, containing a large single-copy region (83,675 bp), a small single-copy region (18,130 bp), and two inverted repeats regions (25,193 bp). The overall GC content of this plastome was 37.

sp. nov., isolated from deep seawater of the Mariana Trench.

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.

Comparative Transcriptome Analysis of Halophyte in Response to Salinity Stress.

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress.

MDN1 Is Involved in the Establishment of a Normal Seed Proteome and Seed Germination.

Seed germination and formation are the beginning and ending, respectively, of a plant life cycle. These two processes are under fine regulation by the internal genetic information. Previously, we demonstrated that MIDASIN 1 (MDN1) is required for ribosome biogenesis, and its dysfunction leads to pleiotropic developmental phenotypes, including impaired embryogenesis and slow seed germination.

Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat.

Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.

The complete chloroplast genome of an annual halophyte herb, (Amaranthaceae).

The complete chloroplast genome (plastome) of , an annual halophytic herb, was determined in this study. The plastome was 149,807 bp in size, containing a large single-copy region (82,162 bp), a small single-copy region (18,191 bp), and two inverted repeats regions (24,727 bp). The overall GC content of this plastome was 36.