DOI: 10.5061/dryad.m37pvmdd0
title: Data on mitochondrial genome rearrangement patterns, annotation resources, and phylogenetic visualization in Actinopteri (ray-finned fishes)

description: This dataset integrates structural variations, annotation resources, and
 phylogenetic analysis results of mitochondrial genomes in ray-finned
 fishes (Actinopterygii). The raw data were sourced from publicly available
 mitochondrial genome records in NCBI GenBank
 (0_gb_actinopteri_14092_from_NCBI.gb), comprising 14,092 original
 sequences. Standardized annotations were generated using the MITOS online
 tool, resulting in a compressed package (1_fasta_bed_actinopteri.zip)
 containing FASTA sequences and BED annotation files, which can be imported
 into Geneious software for visualizing gene structures and boundaries. For
 cases where discrepancies were found between NCBI annotations and MITOS
 results, a Geneious-formatted validation file
 (2_geneious_alignment_validation_files.geneious) is provided, including
 manually corrected alignment evidence. The final compiled CSV
 file systematically organizes taxonomic information, gene
 rearrangement patterns (e.g., ND5-ND6 inversion clusters, tRNA
 translocations), and their associations with order/family-level
 phylogenetic branches for 10,664 genomes. Additionally, a visualization
 file (4_Fish-phy.png) is included, displaying the distribution of gene
 rearrangement events on a phylogenetic tree for intuitive interpretation.
 This dataset is suitable for studies on mitochondrial genome structural
 evolution, annotation pipeline validation, comparative genomics, and
 molecular phylogenetic analysis. All data comply with NCBI GenBank usage
 terms, involve no ethical concerns.
description: # Data on mitochondrial genome rearrangement patterns, annotation
 resources, and phylogenetic visualization in Actinopteri (ray-finned
 fishes) Dataset DOI: [10.5061/dryad.m37pvmdd0](10.5061/dryad.m37pvmdd0) ##
 Description of the data and file structure This dataset is suitable for
 studies on mitochondrial genome structural evolution, annotation pipeline
 validation, comparative genomics, and molecular phylogenetic analysis. All
 data comply with NCBI GenBank usage terms, involve no ethical concerns.
 ### Files and variables #### File:
 2\_geneious\_alignment\_validation\_files.geneious **Description:** Manual
 verification process for discrepancies between NCBI and MITOS annotations.
 #### File: 4\_Fish-phy.png **Description:** Phylogenetic tree with
 annotated gene rearrangement events. #### File:
 0\_gb\_actinopteri\_14092\_from\_NCBI.gb **Description:** Original
 mitochondrial genome records of ray-finned fishes downloaded from NCBI.
 #### File: 1\_fasta\_bed\_actinopteri.zip **Description:** FASTA sequences
 and BED annotation files generated by MITOS, supporting visualization and
 analysis in Geneious. #### File:
 3\_2\_Fish-10664-Gene\_order-Type\_Sta.csv **Description:** This sheet
 contains a visual representation in the form of a pie chart that
 illustrates the proportion of different rearrangement types within the
 dataset. ##### Variables * :Classify the given numbers based on the
 changes in gene sequence order. * Type:The classification based on gene
 rearrangement is divided into five major categories: Short, Type1,
 Rearranged, GAP, and Unsure. * Count:The number of data entries for each
 major category. #### File: 3\_1\_Fish-10664-Gene\_order-All\_Samples.csv
 **Description:** a comprehensive summary table that lists the basic
 information for all data samples, encompassing a total of 10,664 entries.
 ##### Variables * LOCUS:Each piece of data has a unique identifier, which
 can be used to search. * Order:Order * Family:Family * Genus:Genus *
 Species_name:Species_name * Length:The full length of the mitochondrial
 genome refers to the number of base pairs. * GeneOder Type No.:Classify
 the given numbers based on the changes in gene sequence order. * Gene
 Order (exclude CR) annotation from ncbi or mitos:The gene arrangement
 order after inspection (excluding CR). #### File:
 3\_5\_Fish-10664-Gene\_order-ByOrder-73.csv **Description:** This sheet
 provides a statistical analysis of rearrangement types, categorized by the
 biological order classification. ##### Variables * Order:Order * Number of
 families:The number of Families included under each Order. * Number of
 samples:The number of samples included under each Order. * GeneOder Type
 No.:the gene rearrangement types (represented by numbers, corresponding to
 Gene Rearrangement Types in Table 3-3) included under each Order have been
 counted. #### File: 3\_3\_Fish-10664-Gene\_order-Type.csv
 **Description:** The focus of this sheet is on the methodology used to
 assign unique rearrangement numbers to genes based on their sequential
 order. ##### Variables * GeneOder Type No.:Classify the given numbers
 based on the changes in gene sequence order. * NOTE:A brief description of
 the gene rearrangement types and rearrangement positions. * Gene Order
 (exclude CR) annotation from ncbi or mitos:The gene arrangement order
 after inspection (excluding CR). * Count:Statistics of the data counts for
 different GeneOrder Types. #### File:
 3\_4\_Fish-10664-Gene\_order-ByFamily-676.csv **Description:** this sheet
 delves into the statistics of rearrangement types, organized by the
 biological family classification. ##### Variables * Order:Order *
 Family:Family * Count:The number of data entries under each subcategory of
 the hierarchical classification has been counted. * GeneOder Type No.:The
 gene rearrangement types (represented by numbers, corresponding to Gene
 Rearrangement Types in Table 3-3) included under each Family have been
 counted. #### File: 3\_6\_Fish-10664-Gene\_order-Hotspot\_Area\_Sta.csv
 **Description:** This table provides statistics on the frequently
 rearranged positions. ##### Variables * Hotspot/Mix-hotspot:Codes have
 been assigned to some regions where rearrangements frequently occur. *
 NOTE:Describe the regions with different codes. * GeneOder Type
 No.:Classify the given numbers based on the changes in gene sequence
 order. * Count:number