Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

Guan, Wenzhi; Qiu, Gao‐Feng; Feng-Liu,

doi:10.1371/journal.pone.0240308

Cited by 29 publications

(15 citation statements)

References 57 publications

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“…In addition, predicted protein sequences were mapped against several previously published growth- and immune-related genes based on literature review (Overturf et al, 2010; Palti, 2011; Vagner & Santigosa, 2011; Zhenzhen et al, 2014; Hu et al, 2016; Ma et al, 2016; Chandhini & Rejish, 2019; Lin et al, 2019; Dam et al, 2020; Damzamnn et al, 2020; Guan & Qiu, 2020). 82 growth- and 31 immune-related genes (113 genes in total) were downloaded from the NCBI GenBank database (https://www.ncbi.nlm.nih.gov/) and used as references.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

Lau¹,

Lim²,

Chung³

et al. 2022

Preprint

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The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.5 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 84.3%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 53 Actinopterygii species and two outgroups was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.

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Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

Lau¹,

Lim²,

Chung³

et al. 2022

Preprint

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“…73 growth-related genes and 30 immune-related genes were selected based on literature review [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] . Each gene was searched for its respective accession number compatible to its protein sequence in NCBI ( https://www.ncbi.nlm.nih.gov/ ).…”

Section: Data Descriptionmentioning

confidence: 99%

“…Protein marked with * asterisk sign were proteins selected after e -value cutoff while best parameters were inputed for proteins that did not pass the cutoff filter. Contig ID Protein Accession Blast Hit Aligned Length Similarity (%) Reference TRINITY_DN2932_c0_g1_i4.p1 *Acetyl-CoA carboxylase alpha (Haplotype 1) ADT82650.1 15 2342 74.552 [7] TRINITY_DN2318_c0_g1_i1.p1 *Acetyl-CoA carboxylase alpha (Haplotype 2) ADX43925.1 15 2390 96.987 [7] TRINITY_DN2932_c0_g1_i4.p1 *Acetyl-CoA carboxylase 2 XP_018962132.1 20 1837 96.788 [7] TRINITY_DN1703_c0_g1_i1.p1 *Acetyl-CoA Acetyltransferase 2 AAD34966.1 13 395 91.899 [8] TRINITY_DN1946_c0_g2_i1.p1 *Alpha actinin 3 XP_031588180.1 189 896 93.973 [6] TRINITY_DN2816_c0_g1_i1.p1 *ATP synthase BAA82837.1 10 518 99.421 [5] TRINITY_DN7716_c0_g1_i1.p1 *G2/mitotic-specific cyclin-B1 NP_571588.1 27 397 94.71 [7] TRINITY_DN7305_c0_g1_i14.p1 *Cell division cycle protein 20 NP_998245.2 460 496 90.524 [7] TRINITY_DN9513_c0_g1_i1.p1 *Conserved Edge Expressed ABK35126.2 2 322 91.304 [11] TRINITY_DN148_c0_g1_i1.p1 *Creatine kinase M-type …”

Section: Data Descriptionmentioning

confidence: 99%

The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra)

et al. 2021

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The Javan mahseer ( Tor tambra ) is one of the most valuable freshwater fish found in Tor species. To date, other than mitogenomic data (BioProject: PRJNA422829), genomic and transcriptomic resources for this species are still lacking which is crucial to understand the molecular mechanisms associated with important traits such as growth, immune response, reproduction and sex determination. For the first time, we sequenced the transcriptome from a whole juvenile fish using Illumina NovaSEQ6000 generating raw paired-end reads. De novo transcriptome assembly generated a draft transcriptome (BUSCO5 completeness of 91.2% [Actinopterygii_odb10 database]) consisting of 259,403 putative transcripts with a total and N50 length of 333,881,215 bp and 2283 bp, respectively. A total count of 77,503 non-redundant protein coding sequences were predicted from the transcripts and used for functional annotation. We mapped the predicted proteins to 304 known KEGG pathways with signal transduction cluster having the highest representation followed by immune system and endocrine system. In addition, transcripts exhibiting significant similarity to previously published growth-and immune-related genes were identified which will facilitate future molecular breeding of Tor tambra .

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“…On the other hand, driven by declining costs, RNA-seq is becoming increasingly accessible to labs with modest resources; and as a result, it is being employed on an ever-expanding catalog of non-model organisms, pervading the fields of agriculture, aquaculture, ecology, and environment. A very short list of recent studies include: environmental stress response in sea-trout [ 3 ], coral [ 4 ], ryegrass [ 5 ], pigeonpea [ 6 ], tiger barb [ 7 ]; immune response to parasites and pathogens in guppy [ 8 ], eel [ 9 ], silkworm [ 10 ], peanut [ 11 ], sunflower [ 12 ]; mechanisms of phenotypic divergence in hares [ 13 ], bats [ 14 ], grass carps [ 15 ]; effect of diet in the growth and development in shrimp [ 16 ], yellow perch [ 17 ], mandarin fish [ 18 ], grenadier anchovy [ 19 ], catfish [ 20 ], tilapia [ 21 ], bass [ 22 ]. It is only likely that RNA-seq will continue to rapidly proliferate while high-quality reference databases grow at a slow pace.…”

Section: Introductionmentioning

confidence: 99%

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

2022

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Background RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery. Results We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs – the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar. Conclusions The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.

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Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

Cited by 29 publications

References 57 publications

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra)

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

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