ReviewNature protocols2024
Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
80 citing papers in PubMed.
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Genome-Wide Characterization of the Myostatin Gene (MSTN) Ligand-Receptor System and Its Expression Patterns Associated with Growth Variation inInternational journal of molecular sciences · 2026Article
- Genome-Wide Identification of the Glycosyltransferase 4 Family and Characterization ofCurrent issues in molecular biology · 2026Article
- Genome-Wide Analysis ofJournal of fungi (Basel, Switzerland) · 2026Article
- PbrFEN-1 positively regulates pear pollen tube growth and is involved in the self-incompatibility response.Plant reproduction · 2026Article
- Addendum: Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.Nature protocols · 2026Article
- Genome-wide identification and expression profiling of the ERF subfamily in Polygala tenuifolia seedlings under drought stress.BMC plant biology · 2026Article
- Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.BMC plant biology · 2026Article
- Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes.The Plant journal : for cell and molecular biology · 2026Article
- Genome-wide association study and evolutionary analysis of the CrRLK1L family reveal BnCrRLK1L1_5 as a positive regulator of Sclerotinia sclerotiorum resistance in Brassica napus.BMC plant biology · 2026Article
- A chromosome level genome assembly of the marine flowering plant, Torrey's surfgrass (Phyllospadix Torreyi) reveals an exceptionally large Y-chromosome.The Journal of heredity · 2026Article
- Pangenome-wide identification of chloroplast RNA splicing and ribosome maturation (CRM) genes in eight Pyrus genomes indicated their involvement in multiple stresses.Scientific reports · 2026Article
- The Genome of the Rice Variety Mowanggu Provides Insight Into Resistance to Magnaporthe oryzae.Molecular plant pathology · 2026Article
- Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis.Nature communications · 2026Article
- Characteristics of C4-Type Zinc Finger Proteins in Tardigrades and Their Responses in Extreme Environments.International journal of molecular sciences · 2026Article
- Chromosome-Level Sex-Specific Genome Assemblies of Onthophagus binodis Provide Insight into Scarab Sex Chromosomes.Genome biology and evolution · 2026Article
- Genome Assembly of Three Shrub Mangroves in the Genus Acanthus Reveals Two Polyploidy Events and Expansion of Genes Linked to Root Adaptation in Coastal Habitats.GigaScience · 2026Article
- Comprehensive genomic analysis of BAHD gene family: expression patterns during development and stress responses in pecan (Carya illinoinensis).BMC genomics · 2026Article
- Insight into the sulfate transporter gene family in Nicotiana tabacum and functional analysis of NtSULTR1;3 in response to salt stress.BMC plant biology · 2026Article
- Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.Science advances · 2026Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.