A5040215911- Genomics and Phylogenetic Studies
- Plant and Fungal Species Descriptions
- Plant Diversity and Evolution
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Plant Ecology and Taxonomy Studies
- Plant Taxonomy and Phylogenetics
- Plant Pathogens and Fungal Diseases
- Plant Parasitism and Resistance
- Legume Nitrogen Fixing Symbiosis
- Plant Pathogens and Resistance
- Plant and animal studies
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Plant Gene Expression Analysis
- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Yeasts and Rust Fungi Studies
- Microbial Metabolites in Food Biotechnology
- Biochemical and Structural Characterization
- Wheat and Barley Genetics and Pathology
- Plant biochemistry and biosynthesis
- Plant and Fungal Interactions Research
- Agronomic Practices and Intercropping Systems
- Genetic and Environmental Crop Studies
Kunming Institute of Botany
2017-2024
Shandong Normal University
2019-2023
Shandong Academy of Agricultural Sciences
2023
Northwest A&F University
2021-2022
Chinese Academy of Sciences
2017-2019
Jiangsu Academy of Agricultural Sciences
2019
University of Chinese Academy of Sciences
2017
Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although rapid development high-throughput sequencing technology has led to an explosion plastome sequences, annotation remains a significant bottleneck plastomes. User-friendly batch multiple plastomes is urgent need.We introduce Plastid Genome Annotator (PGA), standalone command line tool that can perform rapid, accurate, flexible newly...
Abstract Using DNA barcoding for species identification remains challenging many plant groups. New sequencing approaches such as complete plastid genome may provide some increased power and practical benefits beyond standard barcodes. We undertook a case study comparing to discrimination in the ecologically economically important family Lauraceae, using 191 genomes 131 from 25 genera, representing largest plastome data set Lauraceae date. found that sequences were useful correcting errors...
Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which a Traditional Chinese Medicine (TCM) that utilized as an antifebrile and detoxicant agent for treatment acute pyogenic infections. Historically, many species with violet flowers have been misused in Ding". recognized taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. adulterants were sampled. A total 24 complete chloroplast (cp) genomes analyzed, among these 5...
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few species have been reported to contain isomeric plastomes, but whether the existence is ubiquitous remains be investigated with broader taxon sampling. In this study, we sequenced complete ten Cupressoideae, largest subfamily. Cupressoideae showed relatively accelerated rates substitutions at both nonsynonymous and synonymous sites as...
Abstract Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses plastid protein-coding gene matrix revealed both J C with much longer stem branches than those HCX, so their sister may be attributed to LBA. We used multiple measures including data filtering modifying, evolutionary model...
Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report plastome only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, which 33 encode proteins, 31 tRNAs, and four rRNAs in a 85.3-kb length, has both smallest functionally least capable plastid genome gymnosperms. Although heterotroph retains chlorophyll, all genes are physically or lost, making photosynthetic energy gain...
The plastome (plastid genome) represents an indispensable molecular data source for studying plant phylogeny and evolution. Although size is much smaller than that of nuclear genome, accurate efficient annotation use sequences are not simple tasks. Therefore, a streamlined phylogenomic pipeline from to phylogenetic reconstruction comparative genomics would greatly facilitate research using this important organellar genome. Here we develop PlastidHub, new web application primarily uses novel...
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 species were newly sequenced and used to resolve phylogenetic relationships within Eragrostideae. Including seven reported from Eragrostideae, genome structure, number type genes, codon usage, repeat sequences 20 analyzed. The length these varied 130,773 bp 135,322 bp. These showed typical quadripartite including large single-copy region...
Abstract Background and Aims The Araceae are one of the most diverse monocot families with numerous morphological ecological novelties. Plastid mitochondrial genes have been used to investigate phylogeny interpret shifts in pollination biology biogeography Araceae. In contrast, role whole-genome duplication (WGD) evolution eight subfamilies remains unclear. Methods New transcriptomes or low-depth sequences 65 species were generated through Illumina sequencing. We reconstructed phylogenetic...
Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, playing important role in plant development stress tolerance. However, functions INV genes wheat have been less studied. In this study, a total 126 TaINV were identified using genome-wide search method, which could be classified five classes (TaCWI-α, TaCWI-β, TaCI-α, TaCI-β, TaVI) based on phylogenetic relationship. A 101 TaINVs collinear with their ancestors synteny analysis, we speculated that...
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, plastomes Aristida adscensionis Stipagrostis pennata were newly sequenced, total 16 compared. All conservative genome size, gene number, structure, IR boundary. Repeat sequence analysis showed that forward palindrome repeats most common repeat types. The number SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage plastome...
Calocedrus rupestris is listed as endangered on the IUCN Red List. In this study, we report complete chloroplast genome (plastome) of C. rupestris. The plastome was 127,298 bp in length and encodes 118 unique genes, including 83 protein-coding genes (PCGs), 31 tRNAs, 4 rRNAs. Nine PCGs contained one intron each two introns each. Six tRNAs overall GC content 34.8%. phylogenomic analysis revealed that sister to macrolepis formosana with strong support.
Plant fruit is an important source of natural active phytonutrients that are profitable for human health. Elm (Ulmus pumila) considered as plant food in China rich nutrients. In the present study, high-throughput RNA sequencing was performed U. pumila edible fruits and leaves 11,386 unigenes were filtered dysregulated genes samples, including 5231 up- 6155 downregulated genes. Hundreds pathways predicted to participate seed development phytonutrient biosynthesis by GO, MapMan, KEGG...
Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of and relationships among taxa remain controversial for a long time. To resolve the intra- inter-generic , plastomes 12 (including 8 species 4 varieties), one Orinus species, 15 Triodia two Tripogon Aeluropus were included in present study. All showed similar pattern plastome structure, gene order, content, IR boundaries. number simple sequence repeats ranged from 145...
Summary Flowering plant lineages display remarkable diversity in life history and morphological form. However our understanding of how this phenotypic or disparity, arises what, if any, relation there is to processes such as gene genome duplication remains unlcear. Here we investigate the relationship between genomic evolution angiosperm order Fagales, a lineage woody plants that has been dominant component temperate subtropical forests since Late Cretaceous. To end, examine newly generated...
The complete chloroplast genome (plastome) of Suaeda glauca, an annual halophytic herb, was determined in this study. plastome 149,807 bp size, containing a large single-copy region (82,162 bp), small (18,191 and two inverted repeats regions (24,727 bp). overall GC content 36.5%. In total, 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs 4 rRNAs, were annotated. Phylogenomic analysis showed that S. glauca sister to other species.
The rambler Rosa wichuraiana Crép. is an important founder species during modern rose domestication. However, the chloroplast genome (plastome) of this wild remains unavailable. Here, we assembled complete genomes for two genotypes R. wichuraiana. Both plastomes were typical quadripartite circular with 156,500/156,504 bp in length, comprising a large single-copy (LSC) region 85,651/85,660 and small (SSC) 18,751/18,744 bp, separated by inverted repeat (IR) regions 26,049/26,050 respectively....