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Kim H, Choo H, Cha J, Jang M, Son J, Jeong T, Choi BH, Lim Y, Chai HH, Lee J, Lim D, Shin D, Park W, Park JE. Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens. Anim Cells Syst (Seoul) 2022; 26:358-368. [PMID: 36605592 PMCID: PMC9809412 DOI: 10.1080/19768354.2022.2146187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p < 0.05) enriched, which were limb development, inner ear development, positive regulation of dendrite development, the KEGG pathway the TGF-beta signaling pathway, and melanogenesis (p < 0.05). These pathways are related to morphological maintenance and growth of the tissues. In addition, the SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r 2 = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.
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Affiliation(s)
- Hana Kim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Hyojun Choo
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, Korea
| | - Jihye Cha
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Myoungjin Jang
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Juhwan Son
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Taejoon Jeong
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Youngjo Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Han-Ha Chai
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Korea
| | - Woncheoul Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
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Westbury MV, De Cahsan B, Shepherd LD, Holdaway RN, Duchene DA, Lorenzen ED. Genomic insights into the evolutionary relationships and demographic history of kiwi. PLoS One 2022; 17:e0266430. [PMID: 36215252 PMCID: PMC9550048 DOI: 10.1371/journal.pone.0266430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
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Affiliation(s)
- Michael V. Westbury
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MVW); (EDL)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Richard N. Holdaway
- Palaecol Research Ltd, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | | | - Eline D. Lorenzen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MVW); (EDL)
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Shen S, Chen X, Zhuo Q, Ma Y, Wang J, Wang L, Gong Z, Huo J. Integrating untargeted metabolites and targeted analysis for discrimination of kiwifruits from different cultivars. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Physicochemical, nutritional, and bioactive properties of pulp and peel from 15 kiwifruit cultivars. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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5
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Charlesworth D. The timing of genetic degeneration of sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200093. [PMID: 34247501 DOI: 10.1098/rstb.2020.0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
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6
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De Cahsan B, Westbury MV. Complete mitochondrial genomes offer insights into the evolutionary relationships and comparative genetic diversity of New Zealand’s iconic kiwi (Apteryx spp.). NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1766520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Binia De Cahsan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael V. Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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Waits DS, Simpson DY, Sparkman AM, Bronikowski AM, Schwartz TS. The utility of reptile blood transcriptomes in molecular ecology. Mol Ecol Resour 2019; 20:308-317. [PMID: 31660689 DOI: 10.1111/1755-0998.13110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 02/02/2023]
Abstract
Reptiles and other nonmammalian vertebrates have transcriptionally active nucleated red blood cells. If blood transcriptomes can provide quantitative data to address questions relevant to molecular ecology, this could circumvent the need to euthanize animals to assay tissues. This would allow longitudinal sampling of animals' responses to treatments, as well as sampling of protected taxa. We developed and annotated blood transcriptomes from six reptile species and found on average 25,000 proteins are being transcribed in the blood, and there is a CORE group of 9,282 orthogroups that are found in at least four of six species. In comparison to liver transcriptomes from the same taxa, approximately two-thirds of the orthogroups were found in both blood and liver; and a similar percentage of ecologically relevant gene groups (insulin and insulin-like signalling, electron transport chain, oxidative stress, glucocorticoid receptors) were found transcribed in both blood and liver. As a resource, we provide a user-friendly database of gene ids identified in each blood transcriptome. Although on average 37% of reads mapped to haemoglobin, importantly, the majority of nonhaemoglobin transcripts had sufficient depth (e.g., 97% at ≥10 reads) to be included in differential gene expression analysis. Thus, we demonstrate that RNAseq blood transcriptomes from a very small blood sample (<10 μl) is a minimally invasive option in nonmammalian vertebrates for quantifying expression of a large number of ecologically relevant genes that would allow longitudinal sampling and sampling of protected populations.
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Affiliation(s)
- Damien S Waits
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Dasia Y Simpson
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | | | - Anne M Bronikowski
- Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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Wang Y, Guo J, Wang L, Tian H, Sui J. Transcriptome analysis revealed potential mechanisms of differences in physiological stress responses between caged male and female magpies. BMC Genomics 2019; 20:447. [PMID: 31159743 PMCID: PMC6547487 DOI: 10.1186/s12864-019-5804-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Under caged conditions, birds are affected more severely by environmental stressors such as dietary structure, activity space, human disturbances, and pathogens, which may be reflected in the gene expression in peripheral blood or other tissues. Elucidating the molecular mechanism of these stress responses will help improve animal welfare. Results In the present study, the blood transcriptomes of six male and five female caged magpies (Pica pica) were sequenced, and a total of ~ 100 Gb in clean reads were generated using the Illumina HiSeq 2000 sequencer. A total of 420,291 unigenes were identified after assembly, of which 179,316 were annotated in five databases, 7471 were assigned to 269 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 566 were assigned to the Clusters of Orthologous Groups (COG) functional classification “defense mechanisms”. Analysis of differentially expressed genes (DEGs) showed that 2657 unigenes were differentially expressed between males and females (q < 0.1), and these DEGs were assigned to 45 KEGG pathways involving stress resistance, immunity, energy metabolism, reproduction, lifespan regulation, and diseases. Further analysis revealed that females might be more sensitive to stress through upregulation of c-Jun N-terminal kinases (JNKs) and 5’AMP-activated protein kinase (AMPK), and were also possibly more sensitive to dynamic changes in energy. Females expressed higher major histocompatibility complex (MHC) class II levels than males, enhancing resistance to pathogens, and the DEGs related to reproduction included MAPK, CaMK, CPEB, and Cdc25. The genes related to stress, energy, and immunity were also likely related to the regulation of longevity. The upregulated JNKs in females might prolong lifespan and relieve antioxidant stress. Females may also activate the AMPK pathway and implement dietary restrictions to prolong lifespan, whereas males may upregulate SIRT1 and CRAB to increase lifespan. Conclusions Female magpies might be more sensitive to stress and dynamic changes in energy thus enhanced resistance to pathogens, and the genes related to stress, energy, and immunity were also possibly related to the regulation of longevity. Further confirmations with techniques such as RT-qPCR and western blot are necessary to validate the above arguments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5804-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Wang
- School of Nature Conservation, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083, China
| | - Jinxin Guo
- School of Nature Conservation, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083, China
| | - Lin Wang
- School of Nature Conservation, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083, China
| | - Hengjiu Tian
- Beijing Wildlife Rescue Center, Shuanghelu No.1, Shunyi District, Beijing, 100029, China
| | - Jinling Sui
- School of Nature Conservation, Beijing Forestry University, Qinghuadonglu No. 35, Haidian District, Beijing, 100083, China.
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10
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Hoelzel AR, Bruford MW, Fleischer RC. Conservation of adaptive potential and functional diversity. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01151-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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