The complete mitochondrial genome of Castanopsis carlesii and Castanea henryi reveals the rearrangement and size differences of mitochondrial DNA molecules.
Castanopsis carlesii is a dominant tree species in subtropical evergreen broad-leaved forests and holds significant ecological value. It serves as an excellent timber tree species and raw material for cultivating edible fungi. Henry Chinquapin (Castanea henryi) wood is known for its hardness and resistance to water and moisture, making it an exceptional timber species. Additionally, its fruit has a sweet and fruity taste, making it a valuable food source. However, the mitogenomes of these species have not been previously reported. To gain a better understanding of them, this study successfully assembled high-quality mitogenomes of C. carlesii and Ca. henryi for the first time.
Pubmed ID: 39428457 RIS Download
Research resources used in this publication
None foundAdditional research tools detected in this publication
- BLASTN (RRID:SCR_001598)
- SAMTOOLS (RRID:SCR_002105)
- GenBank (RRID:SCR_002760)
- NCBI (RRID:SCR_006472)
- Geneious (RRID:SCR_010519)
- MISA (RRID:SCR_010765)
- MAFFT (RRID:SCR_011811)
- Trimmomatic (RRID:SCR_011848)
- Newbler (RRID:SCR_011916)
- Pilon (RRID:SCR_014731)
- Canu (RRID:SCR_015880)
- Tandem Repeats Finder (RRID:SCR_022193)
- pMAT (RRID:SCR_022570)
- CodonW (RRID:SCR_023989)
Antibodies used in this publication
None foundAssociated grants
- Agency: the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University,
Id: 72202200205 - Agency: the Outstanding Youth Scientific Fund of Fujian Agriculture and Forestry University,
Id: XJQ202005
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This is a list of tools and resources that we have found mentioned in this publication.
BLASTN (tool)
RRID:SCR_001598
Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
View all literature mentionsSAMTOOLS (tool)
RRID:SCR_002105
Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsGenBank (tool)
RRID:SCR_002760
NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsNCBI (tool)
RRID:SCR_006472
A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.
View all literature mentionsGeneious (tool)
RRID:SCR_010519
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
View all literature mentionsMISA (tool)
RRID:SCR_010765
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
View all literature mentionsMAFFT (tool)
RRID:SCR_011811
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsTrimmomatic (tool)
RRID:SCR_011848
Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsNewbler (tool)
RRID:SCR_011916
A software package for de novo DNA sequence assembly.
View all literature mentionsPilon (tool)
RRID:SCR_014731
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
View all literature mentionsCanu (tool)
RRID:SCR_015880
Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
View all literature mentionsTandem Repeats Finder (tool)
RRID:SCR_022193
Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.
View all literature mentionspMAT (tool)
RRID:SCR_022570
Open source software suite for analysis of fiber photometry data.
View all literature mentionsCodonW (tool)
RRID:SCR_023989
Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.
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