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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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2
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Rodrigues JR, Roy SW, Sehgal RNM. Novel RNA viruses associated with avian haemosporidian parasites. PLoS One 2022; 17:e0269881. [PMID: 35771829 PMCID: PMC9246168 DOI: 10.1371/journal.pone.0269881] [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: 11/22/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect haemosporidian parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon. By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus. MaRNAV3 had ~59% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and ~63% amino acid identity to MaRNAV2. MaRNAV4 had ~44% amino acid identity to MaRNAV1 and ~47% amino acid identity to MaRNAV2. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax, and now two genera of avian haemosporidians.
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Affiliation(s)
- Jose Roberto Rodrigues
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Scott W. Roy
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
- * E-mail: (RNMS); (SWR)
| | - Ravinder N. M. Sehgal
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
- * E-mail: (RNMS); (SWR)
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Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PLoS Pathog 2020; 16:e1008717. [PMID: 32745123 PMCID: PMC7425995 DOI: 10.1371/journal.ppat.1008717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 08/13/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatocystis is a genus of single-celled parasites infecting, amongst other hosts, monkeys, bats and squirrels. Although thought to have descended from malaria parasites (Plasmodium spp.), Hepatocystis spp. are thought not to undergo replication in the blood–the part of the Plasmodium life cycle which causes the symptoms of malaria. Furthermore, Hepatocystis is transmitted by biting midges, not mosquitoes. Comparative genomics of Hepatocystis and Plasmodium species therefore presents an opportunity to better understand some of the most important aspects of malaria parasite biology. We were able to generate a draft genome for Hepatocystis sp. using DNA sequencing reads from the blood of a naturally infected red colobus monkey. We provide robust phylogenetic support for Hepatocystis sp. as a sister group to Plasmodium parasites infecting rodents. We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion. Our analyses highlight the rapid evolution of genes involved in parasite vector stages, revealing genes that may be critical for interactions between malaria parasites and mosquitoes. Hepatocystis parasites are single-celled organisms, closely related to the Plasmodium species which cause malaria. But Hepatocystis are distinct–unlike Plasmodium they are thought not to replicate in the blood and cause little or no disease in their mammalian hosts. They are transmitted from one host to the next, not by mosquitoes, but by biting midges. In this study we generated a genome sequence for Hepatocystis–the first time this data has ever been produced and analysed for this species. We compared genome sequences of Hepatocystis and Plasmodium, confirming that Hepatocystis is descended from Plasmodium. We strengthened support for the absence of replication in the blood and, in line with this finding, discovered that genes involved in interaction with red blood cells have been lost in Hepatocystis. Our analyses revealed rapid evolution of genes which are active when the parasite is in the insect vector, highlighting those which might be important for understanding interaction between malaria parasites and mosquitoes. Hepatocystis has a fascinating evolutionary story and is a powerful comparator for understanding malaria parasite biology.
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Galen SC, Borner J, Williamson JL, Witt CC, Perkins SL. Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites. Mol Ecol Resour 2019; 20:14-28. [PMID: 31507097 DOI: 10.1111/1755-0998.13091] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/22/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022]
Abstract
Metatranscriptomics is a powerful method for studying the composition and function of complex microbial communities. The application of metatranscriptomics to multispecies parasite infections is of particular interest, as research on parasite evolution and diversification has been hampered by technical challenges to genome-scale DNA sequencing. In particular, blood parasites of vertebrates are abundant and diverse although they often occur at low infection intensities and exist as multispecies infections, rendering the isolation of genomic sequence data challenging. Here, we use birds and their diverse haemosporidian parasites to illustrate the potential for metatranscriptome sequencing to generate large quantities of genome-wide sequence data from multiple blood parasite species simultaneously. We used RNA-sequencing of 24 blood samples from songbirds in North America to show that metatranscriptomes can yield large proportions of haemosporidian protein-coding gene repertoires even when infections are of low intensity (<0.1% red blood cells infected) and consist of multiple parasite taxa. By bioinformatically separating host and parasite transcripts and assigning them to the haemosporidian genus of origin, we found that transcriptomes detected ~23% more total parasite infections across all samples than were identified using microscopy and DNA barcoding. For single-species infections, we obtained data for >1,300 loci from samples with as low as 0.03% parasitaemia, with the number of loci increasing with infection intensity. In total, we provide data for 1,502 single-copy orthologous loci from a phylogenetically diverse set of 33 haemosporidian mitochondrial lineages. The metatranscriptomic approach described here has the potential to accelerate ecological and evolutionary research on haemosporidians and other diverse parasites.
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Affiliation(s)
- Spencer C Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
| | - Janus Borner
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Jessie L Williamson
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Christopher C Witt
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Susan L Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
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Videvall E. Genomic Advances in Avian Malaria Research. Trends Parasitol 2019; 35:254-266. [PMID: 30642725 DOI: 10.1016/j.pt.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
Haemosporidian parasites causing malaria-like diseases in birds are globally distributed and have been associated with reduced host fitness and mortality in susceptible bird species. This group of parasites has not only enabled a greater understanding of host specificity, virulence, and parasite dispersal, but has also been crucial in restructuring the evolutionary history of apicomplexans. Despite their importance, genomic resources of avian haemosporidians have proved difficult to obtain, and they have, as a result, been lagging behind the congeneric Plasmodium species infecting mammals. In this review, I discuss recent genomic advances in the field of avian malaria research, and outline outstanding questions that will become possible to investigate with the continued successful efforts to generate avian haemosporidian genomic data.
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Affiliation(s)
- Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.
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Wang L, Zhu W, Dong Z, Song F, Dong J, Fu J. Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia. Int J Mol Sci 2018; 19:ijms19041209. [PMID: 29659520 PMCID: PMC5979384 DOI: 10.3390/ijms19041209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/30/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022] Open
Abstract
Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log2(fold change)| ≥ 1 and q-value ≤ 0.001) were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11, mc1r and asip—played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia.
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Affiliation(s)
- Lanmei Wang
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Wuxi 214081, China.
| | - Wenbin Zhu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Wuxi 214081, China.
| | - Zaijie Dong
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Wuxi 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| | - Juanjuan Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| | - Jianjun Fu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Wuxi 214081, China.
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Videvall E, Cornwallis CK, Ahrén D, Palinauskas V, Valkiūnas G, Hellgren O. The transcriptome of the avian malaria parasite Plasmodium ashfordi
displays host-specific gene expression. Mol Ecol 2017; 26:2939-2958. [DOI: 10.1111/mec.14085] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/16/2017] [Accepted: 02/17/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Elin Videvall
- Department of Biology; Lund University; Sölvegatan 37 SE-22362 Lund Sweden
| | | | - Dag Ahrén
- Department of Biology; Lund University; Sölvegatan 37 SE-22362 Lund Sweden
- National Bioinformatics Infrastructure Sweden (NBIS); Lund University; Sölvegatan 37 SE-22362 Lund Sweden
| | - Vaidas Palinauskas
- Institute of Ecology; Nature Research Centre; Akademijos 2 LT-08412 Vilnius Lithuania
| | - Gediminas Valkiūnas
- Institute of Ecology; Nature Research Centre; Akademijos 2 LT-08412 Vilnius Lithuania
| | - Olof Hellgren
- Department of Biology; Lund University; Sölvegatan 37 SE-22362 Lund Sweden
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