Insights into response to food intake in anadromous
            <i>Coilia nasus</i>
            through stomach transcriptome analysis

Ma, Fengjiao; Yin, Denghua; Fang, Di‐An; Yang, Yanping; Jiang, Min; You, Lei; Jiali, Tian; Xu, Pao; Li, Kai

doi:10.1111/are.14619

Cited by 8 publications

(11 citation statements)

References 66 publications

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“…To reduce data redundancy and improve assembly efficiency, transcripts with a minimum length of 200 bp were assembled and clustered. Sequence quality was verified via FastQC, including the Q20, Q30 and GC content of the clean data (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/; Jiang, Min, et al., 2019; Ma et al., 2020).…”

Section: Methodsmentioning

confidence: 99%

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Tang

Xia²,

Cai³

et al. 2020

Aquac Res

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The giant freshwater prawn (GFP) Macrobrachium rosenbergii is an economically important aquaculture species in China. In culture, it is common for males to show unique morphotypes, which exhibit distinct heterogenous individual growth. Little information is currently available on the molecular mechanisms underlying growth differences among male morphotypes of GFPs. Thus, we herein aimed to identify key genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of GFPs. We performed transcriptome analyses using RNA‐Seq to compare the following male morphotypes of GFPs: orange claw males, old blue claw males and small males. In total, 97.44 Gb clean data were obtained, and 1,857,760 unigenes were annotated by alignment with public protein databases. Moreover, we found 2,072 and 22,431 differentially expressed genes (DEGs) from the eyestalk and gonads respectively. Gene ontology analyses revealed that ‘system process’ and ‘multicellular organismal process’ were the most enriched in the eyestalk and gonad tissue samples respectively. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that pathways associated with gene regulation may play a key role in GFP growth. To summarize, this study provides a valuable repository of novel transcripts for various male morphotypes of GFPs and gives further insights into the molecular mechanisms underlying growth differences in GFPs, which should promote the breeding of commercially cultivated GFPs.

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Section: Methodsmentioning

confidence: 99%

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Tang

Xia²,

Cai³

et al. 2020

Aquac Res

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“…The introduction of transcriptomics has helped the mechanistic exploration of neuropeptides at the RNA level and the network of interactions. NPY, SS, and CCK have been found to influence feeding behavior, and in recent years new evidence has been found in mammalian ( 24 ), avian ( 85 ), and fish species ( 27 , 29 , 53 , 65 ) using transcriptomics. Among them, NPY is involved in promoting feeding, and analysis of the hypothalamus transcriptome of mice subjected to a daily 2-h heat treatment (36°C) for 14 d suggested that up-regulated neuropeptide Y acted to attenuate reduced food intake ( 24 ).…”

Section: Neuropeptidomics and Gene Editingmentioning

confidence: 99%

“…While the affinity of Y2 with PYYb is about 50 times higher than that of PYYa and the affinity of Y7 with PYYa is about three times lower than that of NPY and PYYb ( 190 , 191 ). In addition, unlike mammalian Y2, the two Y2 family receptors in rainbow trout, Y2 and Y7, are both sensitive to NPY with N-terminal deletion and have minimal binding capacity to NPY ( 13 – 24 , 27 – 29 , 31 , 53 , 65 , 79 , 80 , 83 – 85 ) and NPY ( 18 – 24 , 27 – 29 , 31 , 53 , 65 , 79 , 80 , 83 – 85 ), and neither binds to the mammalian Y2-specific antagonist BIIE0246 ( 207 ).…”

Section: Neuropeptide Y and Somatostatin In Food Intake And Growth Of...mentioning

confidence: 99%

Recent advances in neuropeptide-related omics and gene editing: Spotlight on NPY and somatostatin and their roles in growth and food intake of fish

Huang

2022

Front. Endocrinol.

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Feeding and growth are two closely related and important physiological processes in living organisms. Studies in mammals have provided us with a series of characterizations of neuropeptides and their receptors as well as their roles in appetite control and growth. The central nervous system, especially the hypothalamus, plays an important role in the regulation of appetite. Based on their role in the regulation of feeding, neuropeptides can be classified as orexigenic peptide and anorexigenic peptide. To date, the regulation mechanism of neuropeptide on feeding and growth has been explored mainly from mammalian models, however, as a lower and diverse vertebrate, little is known in fish regarding the knowledge of regulatory roles of neuropeptides and their receptors. In recent years, the development of omics and gene editing technology has accelerated the speed and depth of research on neuropeptides and their receptors. These powerful techniques and tools allow a more precise and comprehensive perspective to explore the functional mechanisms of neuropeptides. This paper reviews the recent advance of omics and gene editing technologies in neuropeptides and receptors and their progresses in the regulation of feeding and growth of fish. The purpose of this review is to contribute to a comparative understanding of the functional mechanisms of neuropeptides in non-mammalians, especially fish.

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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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Insights into response to food intake in anadromous Coilia nasus through stomach transcriptome analysis

Cited by 8 publications

References 66 publications

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Recent advances in neuropeptide-related omics and gene editing: Spotlight on NPY and somatostatin and their roles in growth and food intake of fish

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

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