Functional Genomics Research in Aquaculture: Principles and General Approaches

Liu, Shikai; Sun, Fenyong; Jiang, Yanliang; Wang, Ruijia; Li, Chao; Zhang, Jiaren; Liu, Zhanjiang John

doi:10.1002/9781118350041.ch1

Cited by 5 publications

(4 citation statements)

References 249 publications

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“…The inferred orthologies are useful for genome annotation in catfish, and perhaps also useful for functional inference. Orthology inference of gene functions will prove to be an effective approach for the vast majority of genes with aquaculture species [74]. …”

Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements

et al. 2013

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BackgroundComparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a platform for comparative genomic analysis between catfish and other model teleost fish species. This study aimed to gain understanding of genome organizations and similarities among catfish and several sequenced teleost genomes using linkage group 8 (LG8) as a pilot study.ResultsWith existing genome resources, 287 unique genes were identified in LG8. Comparative genome analysis indicated that most of these 287 genes on catfish LG8 are located on two homologous chromosomes of zebrafish, medaka, stickleback, and three chromosomes of green-spotted pufferfish. Large numbers of conserved syntenies were identified. Detailed analysis of the conserved syntenies in relation to chromosome level similarities revealed extensive inter-chromosomal and intra-chromosomal rearrangements during evolution. Of the 287 genes, 35 genes were found to be duplicated in the catfish genome, with the vast majority of the duplications being interchromosomal.ConclusionsComparative genome analysis is a powerful tool even in the absence of a well-assembled whole genome sequence. In spite of sequence stacking due to low resolution of the linkage and physical maps, conserved syntenies can be identified although the exact gene order and orientation are unknown at present. Through chromosome-level comparative analysis, homologous chromosomes among teleosts can be identified. Syntenic analysis should facilitate annotation of the catfish genome, which in turn, should facilitate functional inference of genes based on their orthology.

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Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements

et al. 2013

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“…Hiện nay chỉ có các công bố sử dụng chỉ thị microsatellite nghiên cứu quần đàn cá tra tự nhiên và gia hóa [9, 20,21] và nghiên cứu định danh các loài cá da trơn bằng mã vạch DNA [31]. Kỹ thuật giải trình tự gen thế hệ mới đã mở ra nhiều cơ hội nghiên cứu hệ gen DNA (genome) và hệ gen chức năng RNA (transcriptome) dễ dàng hơn và đã được ứng dụng nghiên cứu hệ gen cho hơn 30 đối tượng thủy sản có giá trị kinh tế [18]. Trong đó nghiên cứu hệ gen chức năng RNA đơn giản hơn, giúp hiểu biết chi tiết các chức năng sinh học ở mức độ phân tử và có thể xác định được các gen tiềm năng liên quan đến tính trạng quan tâm [29].…”

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A transcriptomic analysis of the kidney tissue of tra catfish (Pangasianodon hypophthalmus) reared in saline condition: de novo assembly, annotation, snp discovery

Thành¹,

Thu²,

Jung³

et al. 2015

V J Bio

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Pangasianodon hypophthalmus is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The current study using Ion Torrent technology generated EST resources from the kidney for Tra catfish reared at a salinity level of 9 ppt. We obtained 2,623,929 reads after trimming and processing with an average length of 104 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 29,940 contigs, and allowing identification of 5,710 putative genes when comppared with NCBI non-redundant database. A large number of single nucleotide polymorphisms (SNPs) were also detected. The sequence collection generated in our study represents the most comprehensive transcriptomic resource for P. hypophthalmus available to date.

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“…In other decapods, this precedence is non-existent (no evidence exists for the early evolution of these traits in marine ancestors of the invading group or a possible pre-adaptive role related to the conquest of freshwater) (Vogt, 2013); all true freshwater crabs and freshwater crayfish exhibit ALD and do not have any planktonic stages, and there is no evidence that ALD can be reversible in these groups (Wowor et al, 2009). Liu et al (2012) argued that a single origin for ALD however, is not possible because evolution of larger and intermediate sized eggs with ALD is effectively correlated with a freshwater life cycle. Wowor et al (2009) claimed that evolution of ALD occurred three times independently or alternatively only once accompanied by two reversals during larval development in saline environments.…”

Section: Evolution Of Life History Traits In Macrobrachium Species Wimentioning

confidence: 99%

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

Lifat¹

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Functional Genomics Research in Aquaculture: Principles and General Approaches

Cited by 5 publications

References 249 publications

Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements

Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements

A transcriptomic analysis of the kidney tissue of tra catfish (Pangasianodon hypophthalmus) reared in saline condition: de novo assembly, annotation, snp discovery

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

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