Si‐Qian Jiao
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View article: Comparative transcriptome analysis and heterologous overexpression indicate that the ZjZOG gene may positively regulate the size of jujube fruit
Comparative transcriptome analysis and heterologous overexpression indicate that the ZjZOG gene may positively regulate the size of jujube fruit Open
View article: Author Correction: Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla
Author Correction: Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla Open
View article: Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla
Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla Open
Ehretia macrophylla Wall, known as wild loquat, is an ecologically, economically, and medicinally significant tree species widely grown in China, Japan, Vietnam, and Nepal. In this study, we have successfully generated a haplotype-resolved…
View article: Integrated physiological, transcriptomic, and metabolomic analyses of drought stress alleviation in Ehretia macrophylla Wall. seedlings by SiO2 NPs (silica nanoparticles)
Integrated physiological, transcriptomic, and metabolomic analyses of drought stress alleviation in Ehretia macrophylla Wall. seedlings by SiO2 NPs (silica nanoparticles) Open
With environmental problems such as climate global warming, drought has become one of the major stress factors, because it severely affects the plant growth and development. Silicon dioxide nanoparticles (SiO 2 NPs) are crucial for mitigat…
View article: Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation
Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation Open
Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plant…
View article: Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’)
Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’) Open
Herbaceous peony is a kind of perennial herbaceous flowering plant and most varieties are highly dependent on ramet propagation. Some varieties, such as Paeonia × ‘Coral Charm’, have characteristics of relatively easy root cutting propagat…
View article: Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’)
Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’) Open
Herbaceous peony is a kind of perennial herbaceous flowering plant and most varieties are highly dependent on ramet propagation. Some varieties, such as Paeonia × ‘Coral Charm’, have characteristics of relatively easy root cutting p…
View article: Variation in Platycladus orientalis (Cupressaceae) Reproductive Output and Its Effect on Seed Orchard Crops’ Genetic Diversity
Variation in Platycladus orientalis (Cupressaceae) Reproductive Output and Its Effect on Seed Orchard Crops’ Genetic Diversity Open
The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertilit…
View article: Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome Open
Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chr…
View article: Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger Open
Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, …
View article: A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes
A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes Open
View article: A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes
A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes Open
All data are stored in plain text (txt) format. Each text file includes the structure information and divergence of intact LTR-RTs detected for a specific plant genome.
View article: The complete mitochondrial genome of an endangered tree: <i>Malania oleifera</i>
The complete mitochondrial genome of an endangered tree: <i>Malania oleifera</i> Open
Malania oleifera is an endangered species found in restricted areas in Karst areas in Southwestern China and is also with significant economic and ecological values. Here, complete mitochondrial genome of M. oleifera was characterized, whi…
View article: Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage
Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage Open
Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from …
View article: Landscape genomics predicts climate change‐related genetic offset for the widespread <i>Platycladus orientalis</i> (Cupressaceae)
Landscape genomics predicts climate change‐related genetic offset for the widespread <i>Platycladus orientalis</i> (Cupressaceae) Open
Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combin…
View article: Local Adaptation and Response of Platycladus orientalis (L.) Franco Populations to Climate Change
Local Adaptation and Response of Platycladus orientalis (L.) Franco Populations to Climate Change Open
Knowledge about the local adaptation and response of forest tree populations to the climate is important for assessing the impact of climate change and developing adaptive genetic resource management strategies. However, such information i…
View article: In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues
In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues Open
View article: Genome sequence of <i>Malania oleifera</i>, a tree with great value for nervonic acid production
Genome sequence of <i>Malania oleifera</i>, a tree with great value for nervonic acid production Open
Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially n…
View article: Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S3. Database matches (full results) for C. gigantea unigenes. (XLSX 1763 kb)
View article: Additional file 7: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 7: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S4. BLASTX hits for all unigenes in the Nr database. (XLSX 4233 kb)
View article: Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S7. Functional enrichment analysis of the specific gene families from C. gigantea. The full list of Gene Ontology (GO) enriched functional categories are shown. (XLSX 108 kb)
View article: Additional file 11: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 11: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S6. KEGG pathway annotations for the assembled unigenes. (XLSX 173 kb)
View article: Additional file 8: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 8: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S5. Swiss-Prot annotations for all unigenes. (XLSX 2954 kb)
View article: Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues
Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues Open
Table S8. Characteristics of the transcriptome assemblies from related conifer species and re-analysis results from TRAPID. (XLSX 19 kb)
View article: Development of novel <scp>EST</scp> ‐ <scp>SSR</scp> markers for <i>Ephedra sinica</i> (Ephedraceae) by transcriptome database mining
Development of novel <span>EST</span> ‐ <span>SSR</span> markers for <i>Ephedra sinica</i> (Ephedraceae) by transcriptome database mining Open
Premise of the Study Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether pro…
View article: Malania oleifera genome assembly and annotation v1
Malania oleifera genome assembly and annotation v1 Open
This protocol includes commands and parameter settings for all our steps on genome assembly, quality assessment of genome assembly, transcriptome assembly from RNA-seq, repeat and gene annotation, ortholog identification, phylogenetic reco…
View article: Predicting Future Seed Sourcing of Platycladus orientalis (L.) for Future Climates Using Climate Niche Models
Predicting Future Seed Sourcing of Platycladus orientalis (L.) for Future Climates Using Climate Niche Models Open
Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering …