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Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes. Sci Rep 2022; 12:16381. [PMID: 36180508 PMCID: PMC9525267 DOI: 10.1038/s41598-022-20763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
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Rodgers BD, Ward CW. Myostatin/Activin Receptor Ligands in Muscle and the Development Status of Attenuating Drugs. Endocr Rev 2022; 43:329-365. [PMID: 34520530 PMCID: PMC8905337 DOI: 10.1210/endrev/bnab030] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Muscle wasting disease indications are among the most debilitating and often deadly noncommunicable disease states. As a comorbidity, muscle wasting is associated with different neuromuscular diseases and myopathies, cancer, heart failure, chronic pulmonary and renal diseases, peripheral neuropathies, inflammatory disorders, and, of course, musculoskeletal injuries. Current treatment strategies are relatively ineffective and can at best only limit the rate of muscle degeneration. This includes nutritional supplementation and appetite stimulants as well as immunosuppressants capable of exacerbating muscle loss. Arguably, the most promising treatments in development attempt to disrupt myostatin and activin receptor signaling because these circulating factors are potent inhibitors of muscle growth and regulators of muscle progenitor cell differentiation. Indeed, several studies demonstrated the clinical potential of "inhibiting the inhibitors," increasing muscle cell protein synthesis, decreasing degradation, enhancing mitochondrial biogenesis, and preserving muscle function. Such changes can prevent muscle wasting in various disease animal models yet many drugs targeting this pathway failed during clinical trials, some from serious treatment-related adverse events and off-target interactions. More often, however, failures resulted from the inability to improve muscle function despite preserving muscle mass. Drugs still in development include antibodies and gene therapeutics, all with different targets and thus, safety, efficacy, and proposed use profiles. Each is unique in design and, if successful, could revolutionize the treatment of both acute and chronic muscle wasting. They could also be used in combination with other developing therapeutics for related muscle pathologies or even metabolic diseases.
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Affiliation(s)
| | - Christopher W Ward
- Department of Orthopedics and Center for Biomedical Engineering and Technology (BioMET), University of Maryland School of Medicine, Baltimore, MD, USA
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Funk EC, Breen C, Sanketi BD, Kurpios N, McCune A. Changes in Nkx2.1, Sox2, Bmp4, and Bmp16 expression underlying the lung-to-gas bladder evolutionary transition in ray-finned fishes. Evol Dev 2021; 22:384-402. [PMID: 33463017 DOI: 10.1111/ede.12354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
The key to understanding the evolutionary origin and modification of phenotypic traits is revealing the responsible underlying developmental genetic mechanisms. An important organismal trait of ray-finned fishes is the gas bladder, an air-filled organ that, in most fishes, functions for buoyancy control, and is homologous to the lungs of lobe-finned fishes. The critical morphological difference between lungs and gas bladders, which otherwise share many characteristics, is the general direction of budding during development. Lungs bud ventrally and the gas bladder buds dorsally from the anterior foregut. We investigated the genetic underpinnings of this ventral-to-dorsal shift in budding direction by studying the expression patterns of known lung genes (Nkx2.1, Sox2, and Bmp4) during the development of lungs or gas bladder in three fishes: bichir, bowfin, and zebrafish. Nkx2.1 and Sox2 show reciprocal dorsoventral expression patterns during tetrapod lung development and are important regulators of lung budding; their expression during bichir lung development is conserved. Surprisingly, we find during gas bladder development, Nkx2.1 and Sox2 expression are inconsistent with the hypothesis that they regulate the direction of gas bladder budding. Bmp4 is expressed ventrally during lung development in bichir, akin to the pattern during mouse lung development. During gas bladder development, Bmp4 is not expressed. However, Bmp16, a paralogue of Bmp4, is expressed dorsally in the developing gas bladder of bowfin. Bmp16 is present in the known genomes of Actinopteri (ray-finned fishes excluding bichir) but absent from mammalian genomes. We hypothesize that Bmp16 was recruited to regulate gas bladder development in the Actinopteri in place of Bmp4.
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Affiliation(s)
- Emily C Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Animal Science Department, Genomic Variation Lab, University of California Davis, Davis, California, USA
| | - Catriona Breen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Bhargav D Sanketi
- Department of Molecular Medicine, Veterinary Medical Center, Cornell University, Ithaca, New York, USA
| | - Natasza Kurpios
- Department of Molecular Medicine, Veterinary Medical Center, Cornell University, Ithaca, New York, USA
| | - Amy McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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4
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Funk EC, Birol EB, McCune AR. Does the bowfin gas bladder represent an intermediate stage during the lung-to-gas bladder evolutionary transition? J Morphol 2021; 282:600-611. [PMID: 33538055 DOI: 10.1002/jmor.21330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/09/2022]
Abstract
Whether phenotypic evolution occurs gradually through time has prompted the search for intermediate forms between the ancestral and derived states of morphological features, especially when there appears to be a discontinuous origin. The gas bladder, a derived character of the Actinopteri, is a modification of lungs, which characterize the common ancestor of bony vertebrates. While gas bladders and lungs are similar in many ways, the key morphological difference between these organs is the direction of budding from the foregut during development; essentially, the gas bladder buds dorsally and the lungs bud ventrally from the foregut. Did the shift from ventral lungs to dorsal gas bladder transition through a lateral-budding stage? To answer this question, the precise location of budding during gas bladder development in bowfin, representing the sister lineage to teleosts, has been debated. In the early 20th-century, it was suggested that the bowfin gas bladder buds laterally from the right wall of the foregut. We used nano-CT scanning to visualize the early development of the bowfin gas bladder to verify the historical studies of gas bladder developmental morphology and determine whether the direction of gas bladder budding in bowfin could be intermediate between ventrally budding lungs and dorsally budding gas bladders. We found that the bowfin gas bladder buds dorsally from the anterior foregut; however, during early development, the posterior gas bladder twists right. As development progresses, the posterior, right-hand twist becomes shallower, and the gas bladder itself shifts toward a mid-dorsal position. The budding site is definitively dorsal, despite the temporary lateral twist of the posterior gas bladder.
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Affiliation(s)
- Emily C Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Genomics Variation Lab, University of California Davis, Davis, California, USA
| | - Eda B Birol
- Department of Architecture, Cornell University, Ithaca, New York, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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5
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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6
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Funk E, Lencer E, McCune A. Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:325-338. [PMID: 32864827 PMCID: PMC8094346 DOI: 10.1002/jez.b.22998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022]
Abstract
How modification of gene expression generates novel traits is key to understanding the evolutionary process. We investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates. Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally.
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Affiliation(s)
- Emily Funk
- Cornell University, Department of Ecology and Evolutionary Biology, 215 Tower Rd, Ithaca, NY 14853
- University of California Davis, Genomic Variation Lab, Animal Science Department, 2235 Meyer Hall, Davis, CA 95616
| | - Ezra Lencer
- University of Colorado Denver - Anschutz Medical Campus, Department of Craniofacial Biology, 12081 East 17 Ave, RC 1 South, Campus Box 8120, Aurora, CO 80045
| | - Amy McCune
- Cornell University, Department of Ecology and Evolutionary Biology, 215 Tower Rd, Ithaca, NY 14853
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Sun J, Zhu K, Guo H, Zhang N, Jiang S, Zhang D. Genome-wide comparative analysis ofbone morphogenetic proteins: genomic structure, phylogeny, and expression patterns in the golden pompano,Trachinotus ovatus(Linnaeus, 1758). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:345-358. [PMID: 31680186 DOI: 10.1007/s10695-019-00721-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Bone morphogenetic proteins (BMPs) play important roles in various physiological processes, especially during the formation and maintenance of various organs. In this study, we first obtained and characterized twenty BMP genes from the Trachinotus ovatus genome (designated as ToBMPs). Sequence alignment and phylogenetic analysis both indicated that the predicted amino acid sequences of ToBMP were highly conserved with corresponding homologs of other species. Moreover, a comparative analysis was performed with seven representative vertebrate genomes and found difference in number of BMP3 genes in different species, which three members, BMP3a, BMP3b-1, and BMP3b-2, existed in diploid T. ovatus, but there were four and two members in tetraploidized Cyprinus carpio (BMP3a-1, BMP3a-2, BMP3b-1, and BMP3b-2) and diploid Danio rerio (BMP3a and BMP3b), respectively. The amino acid alignment and genomic structure analysis of ToBMP3 also suggested that the BMP3 gene had expanded in T. ovatus. Furthermore, tissue expression patterns were assessed for the small intestine, liver, white muscle, brain, spleen, fin, gill, head kidney, stomach, blood, and gonads. It was discovered that BMP1, BMP2, BMP3a, BMP4, BMP6, BMP7b, BMP11, and BMP16 were ubiquitously expressed in all the tissues tested. To study the regulatory function of BMP in response to the intake of different types of food, the expression changes in BMP mRNAs were detected by qRT-PCR, and the results showed that the majority of the BMP genes had the highest mRNA levels in the small intestine and liver after ingesting pelleted feed. Our data provide a useful resource for further studies on how paralogous genes may have different expression profiles in T. ovatus.
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Affiliation(s)
- Jinhui Sun
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Province, Guangzhou, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, Guangdong Province, People's Republic of China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Province, Guangzhou, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, Guangdong Province, People's Republic of China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Province, Guangzhou, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, Guangdong Province, People's Republic of China
| | - Shigui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Province, Guangzhou, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, Guangdong Province, People's Republic of China
| | - Dianchang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Province, Guangzhou, China.
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, Guangdong Province, People's Republic of China.
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8
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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9
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Onimaru K, Kuraku S. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications. Brief Funct Genomics 2019; 17:352-361. [PMID: 29566222 PMCID: PMC6158797 DOI: 10.1093/bfgp/ely008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.
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Affiliation(s)
- Koh Onimaru
- RIKEN Center for Life Science Technologies, Kobe, Hyogo Japan.,Department of biological science, Tokyo Institute of Technology, Tokyo, Japan
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10
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Matsunami M, Suzuki M, Haramoto Y, Fukui A, Inoue T, Yamaguchi K, Uchiyama I, Mori K, Tashiro K, Ito Y, Takeuchi T, Suzuki KIT, Agata K, Shigenobu S, Hayashi T. A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. DNA Res 2019; 26:217-229. [PMID: 31006799 PMCID: PMC6589553 DOI: 10.1093/dnares/dsz003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic and genome editing methods. However, limited genetic information is available for P. waltl. We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. We generated 1.2 billion Illumina reads from a wide variety of samples across 12 different tissues/organs, unfertilized egg, and embryos at eight different developmental stages. These reads were assembled into 1,395,387 contigs, from which 202,788 non-redundant ORF models were constructed. The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Our transcriptome resource is expected to enhance future research employing this emerging model animal for regeneration research as well as for investigations in other areas including developmental biology, stem cell biology, and cancer research. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).
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Affiliation(s)
- Masatoshi Matsunami
- Department of Advanced Genomics and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Okinawa, Japan
| | - Miyuki Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Akimasa Fukui
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-Ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ikuo Uchiyama
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazuki Mori
- Computational Bio Big-Data Open Innovation Lab. (CBBD-OIL), Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Shinjuku-Ku, Tokyo, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Takeuchi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Ken-ichi T Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
- Center for the Development of New Model Organisms, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Toshinori Hayashi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
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11
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Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4. Sci Rep 2019; 9:3136. [PMID: 30816280 PMCID: PMC6395752 DOI: 10.1038/s41598-019-40055-1] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 02/07/2019] [Indexed: 12/05/2022] Open
Abstract
The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.
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12
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Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes. BMC Biol 2018; 16:40. [PMID: 29661185 PMCID: PMC5901865 DOI: 10.1186/s12915-018-0509-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Background Conventionally, comparison among amniotes – birds, mammals, and reptiles – has often been approached through analyses of mammals and, for comparison, birds. However, birds are morphologically and physiologically derived and, moreover, some parts of their genomes are recognized as difficult to sequence and/or assemble and are thus missing in genome assemblies. Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes. Results Herein, we present the whole genome sequences of the Madagascar ground gecko (Paroedura picta), a promising study system especially in developmental biology, and used it to identify changes in gene repertoire across amniotes. The genome-wide analysis of the Madagascar ground gecko allowed us to reconstruct a comprehensive set of gene phylogenies comprising 13,043 ortholog groups from diverse amniotes. Our study revealed 469 genes retained by some reptiles but absent from available genome-wide sequence data of both mammals and birds. Importantly, these genes, herein collectively designated as ‘elusive’ genes, exhibited high nucleotide substitution rates and uneven intra-genomic distribution. Furthermore, the genomic regions flanking these elusive genes exhibited distinct characteristics that tended to be associated with increased gene density, repeat element density, and GC content. Conclusion This highly continuous and nearly complete genome assembly of the Madagascar ground gecko will facilitate the use of this species as an experimental animal in diverse fields of biology. Gene repertoire comparisons across amniotes further demonstrated that the fate of a duplicated gene can be affected by the intrinsic properties of its genomic location, which can persist for hundreds of millions of years. Electronic supplementary material The online version of this article (10.1186/s12915-018-0509-4) contains supplementary material, which is available to authorized users.
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Zheng S, Long J, Liu Z, Tao W, Wang D. Identification and Evolution of TGF-β Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia. Int J Mol Sci 2018; 19:E1154. [PMID: 29641448 PMCID: PMC5979292 DOI: 10.3390/ijms19041154] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/24/2018] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-β ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-β ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-β pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Divya D, Bhattacharya TK, Gnana Prakash M, Chatterjee RN, Shukla R, Guru Vishnu PB, Vinoth A, Dushyanth K. Molecular characterization and expression profiling of BMP 3 gene in broiler and layer chicken. Mol Biol Rep 2018; 45:477-495. [DOI: 10.1007/s11033-018-4184-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/04/2018] [Indexed: 11/29/2022]
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Ramakrishnan Varadarajan A, Mopuri R, Streelman JT, McGrath PT. Genome-wide protein phylogenies for four African cichlid species. BMC Evol Biol 2018; 18:1. [PMID: 29368592 PMCID: PMC5784529 DOI: 10.1186/s12862-017-1072-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species. Results We used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented. Conclusion These phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species. Electronic supplementary material The online version of this article (10.1186/s12862-017-1072-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rohini Mopuri
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - J Todd Streelman
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Patrick T McGrath
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA.
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Zhang WZ, Lan T, Nie CH, Guan NN, Gao ZX. Characterization and spatiotemporal expression analysis of nine bone morphogenetic protein family genes during intermuscular bone development in blunt snout bream. Gene 2017; 642:116-124. [PMID: 29129809 DOI: 10.1016/j.gene.2017.11.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 01/24/2023]
Abstract
Intermuscular bones (IBs) only exist in the myosepta of lower teleosts and its molecular mechanism remains to be clarified. Bone morphogenetic proteins (BMPs) have been demonstrated to be involved in various physiological processes, including bone and cartilage formation. In this study, we firstly obtained and characterized nine bmp genes for Megalobrama amblycephala, which belongs to Cyprinidae and have a certain amount of IBs. Sequence alignment and phylogenetic analysis both documented that the mature proteins of M. amblycephala bmp genes were highly conserved with other corresponding homologs, respectively, indicating that the function of each bmp gene has been conserved throughout evolution. As a step to characterize potential involvement of bmp genes in IB formation and development, spatiotemporal expressions of nine bmp genes (bmp2a, bmp2b, bmp3, bmp4, bmp5, bmp7b, bmp8a, bmp14 and bmp16) were investigated during the key development stages of IBs. During the ossification process from stage I (the IBs haven't emerged) to stage IV (all of the IBs ossified in the tail with the mature morphology), the expression profiles revealed that bmp16 was the most abundant transcript while bmp4 had the lowest abundance. The mRNA levels of bmp3, bmp4, bmp5 and bmp8a increased significantly at stage II, suggesting their roles in stimulating IB formation. The expression of bmp7b reached the highest level at stage III (the rapid period of IB development), suggesting potential involvement of bmp7b in promoting osteoblast differentiation. With the exception of bmp7b and bmp16, most bmp genes appeared a significant increase at IB maturation phase (stage IV), which means that they may play important roles in maintenance of IB morphogenesis. Spatial tissue distribution of bmp genes showed that most bmp genes were observed at the highest level in developing IBs at one year old fish. Spatiotemporal expression patterns suggest the potential key roles of these bmp genes in IBs formation and maintenance in fish, being as possible promoters or inhibitors.
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Affiliation(s)
- Wei-Zhuo Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Tian Lan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Ning-Nan Guan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China.
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Tripathy M, Priyam M, Rai U. Repertoire of bone morphogenetic proteins and growth/differentiation factors in ovary of the Indian wall lizard (Hemidactylus flaviviridis) with emphasis on differential expression and gonadotropic regulation of bmp15 and gdf9. Gen Comp Endocrinol 2017; 253:13-24. [PMID: 28837789 DOI: 10.1016/j.ygcen.2017.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/28/2017] [Accepted: 08/14/2017] [Indexed: 11/23/2022]
Abstract
Analysis of ovarian transcriptome of Indian wall lizard demonstrates the existence of several bone morphogenetic proteins (bmp1, 2, 3, 3b, 7, 8, 15) and growth/differentiation factors (gdf5, 9) for the first time in reptilian ovary. The characterization of putative full-length/partial protein sequences of BMPs (BMP2, 3, 3b, 7, 15) and GDF9 showed high homology of their TGF-β domain with that of other vertebrates while BMP1 bore homology to zinc-dependent metalloprotease. Phylogenetic analyses showed clustering of BMPs and GDF9 from wall lizards with that of squamates lying in close proximity to chelonia, crocodilia and aves. This study also correlates the expression of ovarian bmp15 and gdf9 with folliculogenesis. Level of bmp15 dramatically increased with the onset of follicular growth in early recrudescence and attained peak during late recrudescence whereas gdf9 sharply decreased during recrudescence as compared to regression. Nonetheless, expression of these growth factors decreased appreciably with the formation of vitellogenic follicle during breeding phase. Ovarian expression of bmp15 and gdf9 appeared to be regulated by gonadotropin as bmp15 considerably increased while gdf9 decreased in parallel to follicular development after administration of 3 injections of FSH. Expression of both the growth factors declined with the prolongation of treatment that led to formation of early/late vitellogenic follicle. Our in vitro study revealed stimulatory effect of FSH on expression of bmp15 and gdf9 in early growing, previtellogenic and early vitellogenic follicles. In light of in vitro results, FSH-induced in vivo decline in gene expression seems to be due to some other FSH-induced factor.
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Affiliation(s)
- Mamta Tripathy
- Comparative Immunoendocrinology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Manisha Priyam
- Comparative Immunoendocrinology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Umesh Rai
- Comparative Immunoendocrinology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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18
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Genome wide identification, phylogeny, and expression of bone morphogenetic protein genes in tetraploidized common carp (Cyprinus carpio). Gene 2017. [DOI: 10.1016/j.gene.2017.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Urantowka AD, Kroczak A, Mackiewicz P. The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes. BMC Evol Biol 2017; 17:166. [PMID: 28705202 PMCID: PMC5513162 DOI: 10.1186/s12862-017-1012-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 07/04/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. RESULTS Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration. CONCLUSIONS Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.
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Affiliation(s)
- Adam Dawid Urantowka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, ul. Kożuchowska7, 51-631, Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, 50-383 Wrocław, Poland
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Marques CL, Fernández I, Viegas MN, Cox CJ, Martel P, Rosa J, Cancela ML, Laizé V. Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. Cell Mol Life Sci 2016; 73:841-57. [PMID: 26341094 PMCID: PMC11108344 DOI: 10.1007/s00018-015-2024-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/27/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
BMP2, BMP4 and BMP16 form a subfamily of bone morphogenetic proteins acting as pleiotropic growth factors during development and as bone inducers during osteogenesis. BMP16 is the most recent member of this subfamily and basic data regarding protein structure and function, and spatio-temporal gene expression is still scarce. In this work, insights on BMP16 were provided through the comparative analysis of structural and functional data for zebrafish BMP2a, BMP2b, BMP4 and BMP16 genes and proteins, determined from three-dimensional models, patterns of gene expression during development and in adult tissues, regulation by retinoic acid and capacity to activate BMP-signaling pathway. Structures of Bmp2a, Bmp2b, Bmp4 and Bmp16 were found to be remarkably similar; with residues involved in receptor binding being highly conserved. All proteins could activate the BMP-signaling pathway, suggesting that they share a common function. On the contrary, stage- and tissue-specific expression of bmp2, bmp4 and bmp16 suggested the genes might be differentially regulated (e.g. different transcription factors, enhancers and/or regulatory modules) but also that they are involved in distinct physiological processes, although with the same function. Retinoic acid, a morphogen known to interact with BMP-signaling during bone formation, was shown to down-regulate the expression of bmp2, bmp4 and bmp16, although to different extents. Taxonomic and phylogenetic analyses indicated that bmp16 diverged before bmp2 and bmp4, is not restricted to teleost fish lineage as previously reported, and that it probably arose from a whole genomic duplication event that occurred early in vertebrate evolution and disappeared in various tetrapod lineages through independent events.
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Affiliation(s)
- Cátia L Marques
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Ignacio Fernández
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Michael N Viegas
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Cymon J Cox
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Paulo Martel
- Centre for Molecular and Structural Biomedicine (CBME/IBB-LA), University of Algarve, Faro, Portugal
| | - Joana Rosa
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Vincent Laizé
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal.
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Kuraku S, Feiner N, Keeley SD, Hara Y. Incorporating tree-thinking and evolutionary time scale into developmental biology. Dev Growth Differ 2016; 58:131-42. [PMID: 26818824 DOI: 10.1111/dgd.12258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 01/11/2023]
Abstract
Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.
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Affiliation(s)
- Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | | | - Sean D Keeley
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
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Bone Regeneration Using Bone Morphogenetic Proteins and Various Biomaterial Carriers. MATERIALS 2015; 8:1778-1816. [PMID: 28788032 PMCID: PMC5507058 DOI: 10.3390/ma8041778] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/24/2015] [Accepted: 03/27/2015] [Indexed: 01/28/2023]
Abstract
Trauma and disease frequently result in fractures or critical sized bone defects and their management at times necessitates bone grafting. The process of bone healing or regeneration involves intricate network of molecules including bone morphogenetic proteins (BMPs). BMPs belong to a larger superfamily of proteins and are very promising and intensively studied for in the enhancement of bone healing. More than 20 types of BMPs have been identified but only a subset of BMPs can induce de novo bone formation. Many research groups have shown that BMPs can induce differentiation of mesenchymal stem cells and stem cells into osteogenic cells which are capable of producing bone. This review introduces BMPs and discusses current advances in preclinical and clinical application of utilizing various biomaterial carriers for local delivery of BMPs to enhance bone regeneration.
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Feiner N, Meyer A, Kuraku S. Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene. Genome Biol Evol 2014; 6:1635-51. [PMID: 24951566 PMCID: PMC4122933 DOI: 10.1093/gbe/evu135] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The members of the paired box (Pax) family regulate key developmental pathways in many metazoans as tissue-specific transcription factors. Vertebrate genomes typically possess nine Pax genes (Pax1-9), which are derived from four proto-Pax genes in the vertebrate ancestor that were later expanded through the so-called two-round (2R) whole-genome duplication. A recent study proposed that pax6a genes of a subset of teleost fishes (namely, acanthopterygians) are remnants of a paralog generated in the 2R genome duplication, to be renamed pax6.3, and reported one more group of vertebrate Pax genes (Pax6.2), most closely related to the Pax4/6 class. We propose to designate this new member Pax10 instead and reconstruct the evolutionary history of the Pax4/6/10 class with solid phylogenetic evidence. Our synteny analysis showed that Pax4, -6, and -10 originated in the 2R genome duplications early in vertebrate evolution. The phylogenetic analyses of relationships between teleost pax6a and other Pax4, -6, and -10 genes, however, do not support the proposed hypothesis of an ancient origin of the acanthopterygian pax6a genes in the 2R genome duplication. Instead, we confirmed the traditional scenario that the acanthopterygian pax6a is derived from the more recent teleost-specific genome duplication. Notably, Pax6 is present in all vertebrates surveyed to date, whereas Pax4 and -10 were lost multiple times in independent vertebrate lineages, likely because of their restricted expression patterns: Among Pax6-positive domains, Pax10 has retained expression in the adult retina alone, which we documented through in situ hybridization and quantitative reverse transcription polymerase chain reaction experiments on zebrafish, Xenopus, and anole lizard.
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Affiliation(s)
- Nathalie Feiner
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, GermanyPresent address: Department of Zoology, University of Oxford, United Kingdom
| | - Axel Meyer
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Germany
| | - Shigehiro Kuraku
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, GermanyPresent address: Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Hyogo, Japan
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Kuraku S. Impact of asymmetric gene repertoire between cyclostomes and gnathostomes. Semin Cell Dev Biol 2013; 24:119-27. [DOI: 10.1016/j.semcdb.2012.12.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 12/25/2012] [Indexed: 12/12/2022]
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Feiner N, Murakami Y, Breithut L, Mazan S, Meyer A, Kuraku S. Saltatory evolution of the ectodermal neural cortex gene family at the vertebrate origin. Genome Biol Evol 2013; 5:1485-502. [PMID: 23843192 PMCID: PMC3762194 DOI: 10.1093/gbe/evt104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2013] [Indexed: 02/06/2023] Open
Abstract
The ectodermal neural cortex (ENC) gene family, whose members are implicated in neurogenesis, is part of the kelch repeat superfamily. To date, ENC genes have been identified only in osteichthyans, although other kelch repeat-containing genes are prevalent throughout bilaterians. The lack of elaborate molecular phylogenetic analysis with exhaustive taxon sampling has obscured the possible link of the establishment of this gene family with vertebrate novelties. In this study, we identified ENC homologs in diverse vertebrates by means of database mining and polymerase chain reaction screens. Our analysis revealed that the ENC3 ortholog was lost in the basal eutherian lineage through single-gene deletion and that the triplication between ENC1, -2, and -3 occurred early in vertebrate evolution. Including our original data on the catshark and the zebrafish, our comparison revealed high conservation of the pleiotropic expression pattern of ENC1 and shuffling of expression domains between ENC1, -2, and -3. Compared with many other gene families including developmental key regulators, the ENC gene family is unique in that conventional molecular phylogenetic inference could identify no obvious invertebrate ortholog. This suggests a composite nature of the vertebrate-specific gene repertoire, consisting not only of de novo genes introduced at the vertebrate origin but also of long-standing genes with no apparent invertebrate orthologs. Some of the latter, including the ENC gene family, may be too rapidly evolving to provide sufficient phylogenetic signals marking orthology to their invertebrate counterparts. Such gene families that experienced saltatory evolution likely remain to be explored and might also have contributed to phenotypic evolution of vertebrates.
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Affiliation(s)
- Nathalie Feiner
- Chair for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Germany
| | - Yasunori Murakami
- Department of Biology, Faculty of Science, Ehime University, Matsuyama, Japan
| | - Lisa Breithut
- Chair for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
| | - Sylvie Mazan
- Développement et Evolution des Vertébrés, UMR7150 CNRS and Université Paris 6, Station Biologique, Roscoff, France
| | - Axel Meyer
- Chair for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Germany
| | - Shigehiro Kuraku
- Chair for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Germany
- Present address: Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Japan
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A fish-specific member of the TPPP protein family? J Mol Evol 2012; 75:55-72. [PMID: 23053195 DOI: 10.1007/s00239-012-9521-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 09/24/2012] [Indexed: 02/02/2023]
Abstract
A eukaryotic protein family, the tubulin polymerization promoting proteins (TPPPs), has recently been identified. It has been termed after its first member, TPPP/p25 or TPPP1, which exhibits microtubule-stabilizing function and plays a role in neurodegenerative diseases. In mammalian genomes, two further paralogues, TPPP2 and TPPP3, can be found. In this article, I show that TPPP1 and TPPP3, but not TPPP2, are included in paralogons, on human chromosomes, Hsa5 and Hsa16, respectively. I suggest that the single non-vertebrate tppp gene was duplicated in the first round of whole-genome duplication in the vertebrate lineage giving rise to tppp1 and the precursor of tppp2/tppp3. The existence of a teleost fish-specific fourth paralogue, tppp4, has also been raised, but it is not supported by synteny analysis. Alternatively, the new group can be considered as the fish orthologue of TPPP2. The case that the new group is the consequence of the teleost fish-specific whole-genome duplication (3R) cannot be excluded.
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Kuraku S. Hox gene clusters of early vertebrates: do they serve as reliable markers for genome evolution? GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 9:97-103. [PMID: 21802046 PMCID: PMC5054437 DOI: 10.1016/s1672-0229(11)60012-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/21/2011] [Indexed: 10/27/2022]
Abstract
Hox genes, responsible for regional specification along the anteroposterior axis in embryogenesis, are found as clusters in most eumetazoan genomes sequenced to date. Invertebrates possess a single Hox gene cluster with some exceptions of secondary cluster breakages, while osteichthyans (bony vertebrates) have multiple Hox clusters. In tetrapods, four Hox clusters, derived from the so-called two-round whole genome duplications (2R-WGDs), are observed. Overall, the number of Hox gene clusters has been regarded as a reliable marker of ploidy levels in animal genomes. In fact, this scheme also fits the situations in teleost fishes that experienced an additional WGD. In this review, I focus on cyclostomes and cartilaginous fishes as lineages that would fill the gap between invertebrates and osteichthyans. A recent study highlighted a possible loss of the HoxC cluster in the galeomorph shark lineage, while other aspects of cartilaginous fish Hox clusters usually mark their conserved nature. In contrast, existing resources suggest that the cyclostomes exhibit a different mode of Hox cluster organization. For this group of species, whose genomes could have differently responded to the 2R-WGDs from jawed vertebrates, therefore the number of Hox clusters may not serve as a good indicator of their ploidy level.
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Affiliation(s)
- Shigehiro Kuraku
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany.
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Use and efficacy of bone morphogenetic proteins in fracture healing. INTERNATIONAL ORTHOPAEDICS 2011; 35:1271-80. [PMID: 21698428 PMCID: PMC3167450 DOI: 10.1007/s00264-011-1301-z] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Accepted: 06/04/2011] [Indexed: 01/09/2023]
Abstract
Purpose This review evaluates the application of bone morphogenetic proteins (BMPs) in delayed bone repair, aiming at a broad audience from clinicians to scientists. Next to an overview of the role of the different BMPs, their antagonists and their current applications, special attention is focused on new scientific developments improving the effects of BMP-based therapy for bone repair. Methods Publication searches in PubMed and Embase revealed 850 relevant articles on the criteria ‘BMP’ AND ‘bone repair’ (as of May 2011). The abstracts were carefully reviewed and papers were selected according to the content. Results The resulting publications showed that BMP-2 and BMP-7 are clearly the most extensively evaluated BMPs, in general with positive results on bone healing, comparable to the use of unspecific preparations such as autologous bone grafts or platelet-rich plasma. Conclusions Although the efficacy of BMPs as stimulators of bone repair has been demonstrated in model systems and clinical studies, the use of BMPs to enhance fracture healing in the clinical setting is still controversial. Issues such as when, where and how much of which BMP is the most effective and profitable to use still have to be elucidated. But optimisation of the BMP products used in combination with cheaper production methods will inevitably stimulate the clinical use of BMPs for bone fracture healing in the near future.
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Qiu H, Hildebrand F, Kuraku S, Meyer A. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. BMC Genomics 2011; 12:325. [PMID: 21699680 PMCID: PMC3141671 DOI: 10.1186/1471-2164-12-325] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 06/23/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon. RESULTS Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family. CONCLUSIONS Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.
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Affiliation(s)
- Huan Qiu
- Department of Biology, University of Konstanz, Konstanz, Germany
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Wise SB, Stock DW. bmp2b and bmp4 are dispensable for zebrafish tooth development. Dev Dyn 2011; 239:2534-46. [PMID: 21038444 DOI: 10.1002/dvdy.22411] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Bone morphogenetic protein (Bmp) signaling has been shown to play important roles in tooth development at virtually all stages from initiation to hard tissue formation. The specific ligands involved in these processes have not been directly tested by loss-of-function experiments, however. We used morpholino antisense oligonucleotides and mutant analysis in the zebrafish to reduce or eliminate the function of bmp2b and bmp4, two ligands known to be expressed in zebrafish teeth and whose mammalian orthologs are thought to play important roles in tooth development. Surprisingly, we found that elimination of function of these two genes singly and in combination did not prevent the formation of mature, attached teeth. The mostly likely explanation for this result is functional redundancy with other Bmp ligands, which may differ between the zebrafish and the mouse.
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Affiliation(s)
- Sarah B Wise
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309-0449, USA
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Luckenbach JA, Dickey JT, Swanson P. Follicle-stimulating hormone regulation of ovarian transcripts for steroidogenesis-related proteins and cell survival, growth and differentiation factors in vitro during early secondary oocyte growth in coho salmon. Gen Comp Endocrinol 2011; 171:52-63. [PMID: 21187099 DOI: 10.1016/j.ygcen.2010.12.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/16/2010] [Accepted: 12/20/2010] [Indexed: 11/17/2022]
Abstract
Little is known about follicle-stimulating hormone (FSH) function during oocyte growth in fishes. The goal of this study was to gain a fundamental understanding of FSH action on ovarian follicles during early secondary oocyte growth by examining changes in ovarian gene expression and steroidogenesis in response to FSH. Coho salmon (Oncorhynchus kisutch) mid to late cortical alveolus stage follicles were incubated with or without salmon FSH in time-course and concentration-response experiments. Steroid levels were determined in the culture medium by immunoassay and levels of target ovarian mRNAs were determined by quantitative RT-PCR. Medium estradiol-17β (E2) levels increased in response to FSH and plateaued by 36h, while testosterone levels increased similarly but were lower and more variable than E2. Gonadotropin receptor transcripts were differentially regulated, with fshr and lhcgr being down- and up- regulated, respectively. Transcripts encoding proteins involved in steroidogenesis, such as star and hsd3b were significantly upregulated by FSH, whereas aromatase (cyp19a1a) mRNA was unaffected by FSH and declined over time in culture. A recently identified teleost gene, bmp16, was suppressed by FSH and an anti-apoptotic factor, clusterin 1 (clu1), was upregulated by FSH. Lesser FSH effects were observed on igf2, cyp11a1 and cyp17a1, which were stimulated, and igf1ra, inhbb, amh and apoe, which were suppressed. As evident by the significant increases in steroid production and transcripts for specific steroidogenesis-related proteins, FSH influences steroidogenesis during early secondary growth and may be a critical signal for puberty onset. Effects of FSH on ovarian anti-apoptotic and growth factor genes suggest roles for FSH in cell survival, growth and differentiation in teleosts.
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Affiliation(s)
- J Adam Luckenbach
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA 98112, USA.
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Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish. EvoDevo 2011; 2:1. [PMID: 21205289 PMCID: PMC3024246 DOI: 10.1186/2041-9139-2-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 01/04/2011] [Indexed: 01/03/2023] Open
Abstract
Background Cichlid fishes have undergone rapid, expansive evolutionary radiations that are manifested in the diversification of their trophic morphologies, tooth patterning and coloration. Understanding the molecular mechanisms that underlie the cichlids' unique patterns of evolution requires a thorough examination of genes that pattern the neural crest, from which these diverse phenotypes are derived. Among those genes, the homeobox-containing Dlx gene family is of particular interest since it is involved in the patterning of the brain, jaws and teeth. Results In this study, we characterized the dlx genes of an African cichlid fish, Astatotilapia burtoni, to provide a baseline to later allow cross-species comparison within Cichlidae. We identified seven dlx paralogs (dlx1a, -2a, -4a, -3b, -4b, -5a and -6a), whose orthologies were validated with molecular phylogenetic trees. The intergenic regions of three dlx gene clusters (dlx1a-2a, dlx3b-4b, and dlx5a-6a) were amplified with long PCR. Intensive cross-species comparison revealed a number of conserved non-coding elements (CNEs) that are shared with other percomorph fishes. This analysis highlighted additional lineage-specific gains/losses of CNEs in different teleost fish lineages and a novel CNE that had previously not been identified. Our gene expression analyses revealed overlapping but distinct expression of dlx orthologs in the developing brain and pharyngeal arches. Notably, four of the seven A. burtoni dlx genes, dlx2a, dlx3b, dlx4a and dlx5a, were expressed in the developing pharyngeal teeth. Conclusion This comparative study of the dlx genes of A. burtoni has deepened our knowledge of the diversity of the Dlx gene family, in terms of gene repertoire, expression patterns and non-coding elements. We have identified possible cichlid lineage-specific changes, including losses of a subset of dlx expression domains in the pharyngeal teeth, which will be the targets of future functional studies.
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Bone morphogenetic proteins: a critical review. Cell Signal 2010; 23:609-20. [PMID: 20959140 DOI: 10.1016/j.cellsig.2010.10.003] [Citation(s) in RCA: 489] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 09/14/2010] [Accepted: 10/01/2010] [Indexed: 12/14/2022]
Abstract
Bone Morphogenetic Proteins (BMPs) are potent growth factors belonging to the Transforming Growth Factor Beta superfamily. To date over 20 members have been identified in humans with varying functions during processes such as embryogenesis, skeletal formation, hematopoiesis and neurogenesis. Though their functions have been identified, less is known regarding levels of regulation at the extracellular matrix, membrane surface, and receptor activation. Further, current models of activation lack the integration of these regulatory mechanisms. This review focuses on the different levels of regulation, ranging from the release of BMPs into the extracellular components to receptor activation for different BMPs. It also highlights areas in research that is lacking or contradictory.
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Palaeophylogenomics of the Vertebrate Ancestor--Impact of Hidden Paralogy on Hagfish and Lamprey Gene Phylogeny. Integr Comp Biol 2010; 50:124-9. [DOI: 10.1093/icb/icq044] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Gesemann M, Lesslauer A, Maurer CM, Schönthaler HB, Neuhauss SCF. Phylogenetic analysis of the vertebrate excitatory/neutral amino acid transporter (SLC1/EAAT) family reveals lineage specific subfamilies. BMC Evol Biol 2010; 10:117. [PMID: 20429920 PMCID: PMC2873418 DOI: 10.1186/1471-2148-10-117] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 04/29/2010] [Indexed: 12/03/2022] Open
Abstract
Background The composition and expression of vertebrate gene families is shaped by species specific gene loss in combination with a number of gene and genome duplication events (R1, R2 in all vertebrates, R3 in teleosts) and depends on the ecological and evolutionary context. In this study we analyzed the evolutionary history of the solute carrier 1 (SLC1) gene family. These genes are supposed to be under strong selective pressure (purifying selection) due to their important role in the timely removal of glutamate at the synapse. Results In a genomic survey where we manually annotated and analyzing sequences from more than 300 SLC1 genes (from more than 40 vertebrate species), we found evidence for an interesting evolutionary history of this gene family. While human and mouse genomes contain 7 SLC1 genes, in prototheria, sauropsida, and amphibia genomes up to 9 and in actinopterygii up to 13 SLC1 genes are present. While some of the additional slc1 genes in ray-finned fishes originated from R3, the increased number of SLC1 genes in prototheria, sauropsida, and amphibia genomes originates from specific genes retained in these lineages. Phylogenetic comparison and microsynteny analyses of the SLC1 genes indicate, that theria genomes evidently lost several SLC1 genes still present in the other lineage. The genes lost in theria group into two new subfamilies of the slc1 gene family which we named slc1a8/eaat6 and slc1a9/eaat7. Conclusions The phylogeny of the SLC1/EAAT gene family demonstrates how multiple genome reorganization and duplication events can influence the number of active genes. Inactivation and preservation of specific SLC1 genes led to the complete loss of two subfamilies in extant theria, while other vertebrates have retained at least one member of two newly identified SLC1 subfamilies.
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Affiliation(s)
- Matthias Gesemann
- University of Zurich, Institute of Molecular Life Sciences, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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