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Genome Analysis and Drought Response Study of Albizia Odoratissima

https://doi.org/10.2139/ssrn.4822271
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
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Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits
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Epigenetic responses to drought stress in rice (Oryza sativa L.)
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RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences
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Combined effect of water inundation and heavy metals on the photosynthesis and physiology of Spartina alterniflora
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Effects of drought acclimation on drought stress resistance in potato (Solanum tuberosum L.) genotypes
inferredcites →https://doi.org/10.1016/j.envexpbot.2021.104627openalex-extracted
Transcriptome analysis reveals abscisic acid enhancing drought resistance by regulating genes related to flavonoid metabolism in pigeon pea
inferredcites →https://doi.org/10.1016/j.envexpbot.2023.105232openalex-extracted
ZmTCP14, a TCP transcription factor, modulates drought stress response in Zea mays L
inferredcites →https://doi.org/10.1016/j.molp.2022.10.018openalex-extracted
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
inferredcites →https://doi.org/10.1016/j.tplants.2018.04.001openalex-extracted
ABA Transport and Plant Water Stress Responses
inferredcites →https://doi.org/10.1021/acs.jafc.2c01306openalex-extracted
Switchgrass Metabolomics Reveals Striking Genotypic and Developmental Differences in Specialized Metabolic Phenotypes
inferredcites →https://doi.org/10.1038/nbt.1883openalex-extracted
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nbt.2727openalex-extracted
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
inferredcites →https://doi.org/10.1038/nbt.3122openalex-extracted
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-extracted
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/s41592-020-01056-5openalex-extracted
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
inferredcites →https://doi.org/10.1093/bioinformatics/btn013openalex-extracted
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-extracted
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt509openalex-extracted
Infernal 1.1: 100-fold faster RNA homology searches
inferredcites →https://doi.org/10.1093/hr/uhac275openalex-extracted
MaDREB1F confers cold and drought stress resistance through common regulation of hormone synthesis and protectant metabolite contents in banana
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-extracted
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/mst100openalex-extracted
Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3
inferredcites →https://doi.org/10.1093/molbev/msx148openalex-extracted
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-extracted
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/gkg095openalex-extracted
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
inferredcites →https://doi.org/10.1093/nar/gkg770openalex-extracted
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
inferredcites →https://doi.org/10.1093/nar/gki081openalex-extracted
Rfam: annotating non-coding RNAs in complete genomes
inferredcites →https://doi.org/10.1093/nar/gkj112openalex-extracted
miRBase: microRNA sequences, targets and gene nomenclature
inferredcites →https://doi.org/10.1093/nar/gkj149openalex-extracted
Pfam: clans, web tools and services
inferredcites →https://doi.org/10.1093/nar/gkm286openalex-extracted
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
inferredcites →https://doi.org/10.1093/nar/gkv1070openalex-extracted
KEGG as a reference resource for gene and protein annotation
inferredcites →https://doi.org/10.1093/nar/gkv227openalex-extracted
Identification of protein coding regions in RNA transcripts
inferredcites →https://doi.org/10.1093/nar/gkw092openalex-extracted
Using intron position conservation for homology-based gene prediction
inferredcites →https://doi.org/10.1093/nar/gky1038openalex-extracted
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
inferredcites →https://doi.org/10.1093/nar/gky995openalex-extracted
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1093/plphys/kiac560openalex-extracted
DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice
inferredcites →https://doi.org/10.1093/synbio/ysaa005openalex-extracted
Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges
inferredcites →https://doi.org/10.1101/gr.082081.108openalex-extracted
genBlastA: Enabling BLAST to identify homologous gene sequences
inferredcites →https://doi.org/10.1101/gr.1239303openalex-extracted
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.1865504openalex-extracted
GeneWise and Genomewise
inferredcites →https://doi.org/10.1104/pp.006858openalex-extracted
The Combined Effect of Drought Stress and Heat Shock on Gene Expression in Tobacco
inferredcites →https://doi.org/10.1104/pp.17.01310openalex-extracted
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons
inferredcites →https://doi.org/10.1111/nph.18443openalex-extracted
Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass ( Panicum virgatum )
inferredcites →https://doi.org/10.1111/pbi.13752openalex-extracted
Transcriptional activation of rice CINNAMOYL‐CoA REDUCTASE 10 by OsNAC5, contributes to drought tolerance by modulating lignin accumulation in roots
inferredcites →https://doi.org/10.1126/sciadv.abg4619openalex-extracted
Optogenetic control of the guard cell membrane potential and stomatal movement by the light-gated anion channel Gt ACR1
inferredcites →https://doi.org/10.1186/1471-2105-5-59openalex-extracted
Gene finding in novel genomes
inferredcites →https://doi.org/10.1186/1471-2105-9-18openalex-extracted
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-extracted
WGCNA: an R package for weighted correlation network analysis
inferredcites →https://doi.org/10.1186/1471-2164-15-527openalex-extracted
Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-extracted
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-extracted
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1186/s13059-015-0831-xopenalex-extracted
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
inferredcites →https://doi.org/10.3389/fpls.2022.1020367openalex-extracted
Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance
inferredcites →https://doi.org/10.7235/hort.2015.15054openalex-extracted
Proline, Sugars, and Antioxidant Enzymes Respond to Drought Stress in the Leaves of Strawberry Plants
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