The Asymmetron lucayanum Genome Project

This data repository contains supplementary data files for the Asymmetron lucayanum genome project. 

First of all, 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)

Also, we curated the multi-stage bulk RNA-seq datasets (both from this study and published studies) of five cephalochordate species and mapped them to the corresponding annotated genomes described above. The gene expression profile was summarized by TPM and provided with the following file:cephalochordate_TPM.xlsx