DOI: 10.5281/zenodo.18287544
title: Insights into cephalochordate genome and gene evolution from the early-diverging amphioxus Asymmetron lucayanum

description: This data repository contains the gene annotation files that we generated for five cephalochordate species:



Alu: Asymmetron lucayanum

Bbe: Branchiostoma belcheri 

Bfl: Branchiostoma floridae

Bja: Branchiostoma japonicum

Bla: Branchiostoma lanceolatum


The Alu genome was sequenced by our team (www.evomicslab.org) with collaboration with Dr. Jr-Kai Yu, Dr. Sung-Jin Cho, and Dr. Linda Holland. Two haplotype-decoupled assemblies were produced corresponding to the reference (filename: Asymmetron_lucayanum.ref.*) and alternative (filename: Asymmetron_lucayanum.alt.*). The assembly file of these two genome assemblies have been deposited in Genome Warehouse of National Genomics Data Center (https://ngdc.cncb.ac.cn/gwh) under the accession numbers of GWHFWAS00000000.1 and GWHFWAV00000000.1 respectively.

The Bbe, Bfl, Bja, and Bla genome assemblies were generated by previous studies:




Species
NCBI Genbank accession number
Reference


Bbe
GCA_019207075.1
Huang et al. (2023) Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. PNAS, 120 (10), e2201504120


Bfl
GCA_019207045.1
Huang et al. (2023) Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. PNAS, 120 (10), e2201504120


Bja
GCA_013266295.2
Huang et al. (2023) Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. PNAS, 120 (10), e2201504120


Bla
GCA_927797965.1
Brasó-Vives et al. (2022) Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biology, 23 (1), 243




 

All 6 genome assemblies were annotated with the same annotation pipeline in our study: RepeatMasker (v4.1.1) and EDTA (v2.0.1) for  repeats/TE annotation, FunAnnotate (v1.8.15) for protein coding gene and tRNA gene annotation, RNAmmer (v1.2) for rRNA gene annotation. 

Explanation for each files:

Species_name.gff3.gz  # protein-coding gene and tRNA gene annotation in GFF3 format (compressed by gzip)

Species_name.cds-transcripts.fa.gz  # CDS/transcript sequences of annotated protein-coding genes in FASTA format (compressed by gzip)

Species_name.proteins.fa.gz  # protein sequences of annotated protein-coding genes in FASTA format (compressed by gzip)

Species_name.rRNA.gff2.gz # rRNA gene annotation in GFF2 format (compressed by gzip)

Species_name.TEanno.gff3.gz # TE annotation in GFF3 format (compressed by gzip)

 

In addition, we generated some potentially valuable intermediate and final result files for various comparative genomics analyses. 

AluAsRef_amphioxus_5way_WGA.maf.gz # The multi-way whole-genome alignment files across the five amphioxus species (Alu, Bbe, Bfl, Bja, Bla). The Alu reference genome was used as reference for providing genomic coordinates. 

HsaAsRef_vertebrate_6way_WGA.maf.gz # The multi-way whole-genome alignment files across the fix vertebrate species (spotted gar, frog, chicken, platypus, mouse, human). The human reference genome was used as reference for providing genomic coordinates. 

Alu_ref.Hsa.final.axt.gz # The pairwise whole-genome alignment file between the Alu and human. 

five_amphioxus_Hox_CDS_aln.tar.gz # The full-length CDS alignment for orthologous Hox genes across the five amphioxus species (Alu, Bbe, Bfl, Bja, Bla). 

human_chimpanzee_Hox_CDS_aln.tar.gz # The full-length CDS alignment for orthologous Hox genes between human and chimpanzee.

Hox.protein.untrimmed.fa # The untrimmed full-length protein alignment for the Hox gene family.

Hox.protein.trimmed.fa # The trimmed full-length protein alignment for the Hox gene family.

Hox.protein.trimmed.treefile # The trimmed full-length protein tree (newick format) for the Hox gene family.

TLR.protein.untrimmed.fa # The untrimmed full-length protein alignment for the TLR gene family.

TLR.protein.trimmed.fa # The trimmed full-length protein alignment for the TLR gene family.

TLR.protein.trimmed.treefile # The trimmed full-length protein tree (newick format) for the TLR gene family.

NLR.protein.untrimmed.fa # The untrimmed full-length protein alignment for the NLR gene family.

NLR.protein.trimmed.fa # The trimmed full-length protein alignment for the NLR gene family.

NLR.protein.trimmed.treefile # The trimmed full-length protein tree (newick format) for the NLR gene family.

RAG1.protein.untrimmed.fa # The untrimmed full-length protein alignment for the RAG1(-like) gene family.

RAG1.protein.trimmed.fa # The trimmed full-length protein alignment for the RAG1(-like) gene family.

RAG1.protein.trimmed.treefile # The trimmed full-length protein tree (newick format) for the RAG1(-like) gene family.

RAG2.protein.untrimmed.fa # The untrimmed full-length protein alignment for the RAG2(-like) gene family.

RAG2.protein.trimmed.fa # The trimmed full-length protein alignment for the RAG2(-like) gene family.

RAG2.protein.trimmed.treefile # The trimmed full-length protein tree (newick format) for the RAG2(-like) gene family.

species_phylogeny.protein.trimmed.fa # The concatednated and trimmed protein alingment based on 947 one-to-one orthologous genes.

species_phylogeny.protein.trimmed.treefile # The concatednated and trimmed protein tree based on 947 one-to-one orthologous genes.

 

In addition, the supplementary dataset S1-S8 for this study:

Dataset S1. The correspondence table between new (this study) and old (published study) annotations for the four Branchiostoma species.

Dataset S2. The 5-way pan-cephalochordate microsynteny conservation blocks and those further conserved with human or hagfish.

Dataset S3. The trimmed full-length protein tree (printed version) for the Hox gene family.

Dataset S4. Summary results for the analyses of pan-cephalochordate conserved regions as well as those further shared with vertebrates.

Dataset S5. summary results for the genome-wide scan of TLR and NLR genes in this study

Dataset S6. The trimmed full-length protein tree (printed version) for the TLR gene family.

Dataset S7. The trimmed full-length protein tree (printed version) for the NLR gene family.

Dataset S8. Our curated the multi-stage bulk RNA-seq datasets (both from this study and published studies) of the five cephalochordate species used in this study.

 

Finally, the in-house scripts used for this study:

Asymmetron_Pipelines-main.zip # The in-house scripts used in this study. Also deposited at GitHub (https://github.com/ArthurSilver/Asymmetron_Pipelines).