Supporting data for "Draft genome of Glyptosternon maculatum, an endemic fish from Tibet-plateau"

Dataset type: Genomic
Data released on August 07, 2018

Liu H; Liu Q; Chen Z; Liu Y; Zhou C; Liang Q; Ma C; Zhou J; Pan Y; Chen M; Wangjiu W; Jiang W; Xiao S; Mou Z (2018): Supporting data for "Draft genome of Glyptosternon maculatum, an endemic fish from Tibet-plateau" GigaScience Database. http://dx.doi.org/10.5524/100489

DOI10.5524/100489

Mechanisms for high altitude adaption have arisen widespread interest to evolution biologists. Several genome wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds and amphibians. However, little information was known about the adaptive evolution of highland fishes. Glyptosternon maculatum (G. maculatum, Regan, 1905), also known as Regan or barkley, is a fish endemic to the Tibetan plateau, which belongs to Sisoridae family, Siluriformes (catfishes) order. This species live within an elevation ranging from roughly 2800 m to 4200 m. Hence, a high-quality reference genome of G. maculatum provides an opportunity to address high altitude adaption mechanisms of fishes.
To get a high-quality reference genome of G. maculatum, we combined PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and BioNano optical map techniques. In total, 603.99 Gb sequencing data were generated. The assembled genome was about 662.34 Mb with scaffold and contig N50 sizes of 20.90 Mb and 993.67 kb, respectively, which captured 83% complete and 3.9% partial vertebrate Benchmarking Universal Single-copy orthologs (BUSCO). Repetitive elements account for 35.88% of the genome, and 22,066 protein-coding genes were predicted from the genome, of which 91.7% have been functionally annotated.
We provide the first comprehensive de novo genome of the G. maculatum. This genetic resource is fundamental for investigating the origin of the G. maculatum and will improve our understanding of high altitude adaption of fishes. The assembled genome can also be used as reference for future population genetic studies of G. maculatum.

Additional details

Read the peer-reviewed publication(s):

Liu, H., Liu, Q., Chen, Z., Liu, Y., Zhou, C., Liang, Q., … Mou, Z. (2018). Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. GigaScience, 7(9). doi:10.1093/gigascience/giy104

Accessions (data included in GigaDB):

BioProject: PRJNA447978





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
G.maculatum-DNA175778  Glyptosternon maculatum Description:Genomic DNA extracted from muscle tiss...
Sex:female [NCIT:C16576]
Geographic location (latitude and longitude):29.11...
...
+
RRA61704-S-W175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61705-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61706-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61707-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61708-S-W175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61709-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61710-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61711-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
RRA61712-S175778  Glyptosternon maculatum Description:RNA extracted from the whole embryo at...
Sex:Undetermined [NCIT:C124294]
Geographic location (latitude and longitude):29.11...
...
+
Displaying 1-10 of 11 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsFASTA149.52 MB2018-07-30
annotationGFF47.23 MB2018-07-30
otherTAR51.85 KB2018-07-30
Coding SequenceFASTA9.57 MB2018-07-30
Genome sequenceFASTA179.8 MB2018-07-30
annotationUNKNOWN4.47 MB2018-07-30
protein sequenceFASTA6.19 MB2018-07-30
Phylogenetic treeUNKNOWN0.12 KB2018-07-30
Sequence variantsVCF16.96 MB2018-07-30
ReadmeTEXT2.74 KB2018-07-30
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
Tibet government H Liu 2017CZZX003
National Natural Science Foundation of China H Liu 31560144
National Natural Science Foundation of China S Xiao 31602207
Date Action
August 7, 2018 Dataset publish
August 7, 2018 Description updated from : Mechanisms for high altitude adaption have arisen widespread interest to evolution biologists. Several genome wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds and amphibians. However, little information was known about the adaptive evolution of highland fishes. Glyptosternon maculatum (G. maculatum, Regan, 1905), also known as Regan or barkley, is a fish endemic to the Tibetan plateau, which belongs to Sisoridae family, Siluriformes (catfishes) order. This species live within an elevation ranging from roughly 2800 m to 4200 m. Hence, a high-quality reference genome of G. maculatum provides an opportunity to address high altitude adaption mechanisms of fishes.
To get a high-quality reference genome of G. maculatum, we combined PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and BioNano optical map techniques. In total, 603.99 Gb sequencing data were generated. The assembled genome was about 662.34 Mb with scaffold and contig N50 sizes of 20.90 Mb and 993.67 kb, respectively, which captured 83% complete and 3.9% partial vertebrate Benchmarking Universal Single-copy orthologs (BUSCO). Repetitive elements account for 35.88% of the genome, and 22,066 protein-coding genes were predicted from the genome, of which 91.7% have been functionally annotated.
We provide the first comprehensive de novo genome of the G. maculatum. This genetic resource is fundamental for investigating the origin of the G.maculatum and will improve our understanding of high altitude adaption of fishes. The assembled genome can also be used as reference for future population genetic studies of G. maculatum.
August 22, 2018 Manuscript Link added : 10.1093/gigascience/giy104