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Li J, Han G, Tian X, Liang D, Zhang P. UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics. Mol Biol Evol 2023; 40:msad230. [PMID: 37832226 PMCID: PMC10630340 DOI: 10.1093/molbev/msad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
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Affiliation(s)
- JiaXuan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - GuangCheng Han
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao Tian
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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Li J, Liang D, Zhang P. Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.969581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.
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Kacprzyk J, Locatelli AG, Hughes GM, Huang Z, Clarke M, Gorbunova V, Sacchi C, Stewart GS, Teeling EC. Evolution of mammalian longevity: age-related increase in autophagy in bats compared to other mammals. Aging (Albany NY) 2021; 13:7998-8025. [PMID: 33744862 PMCID: PMC8034928 DOI: 10.18632/aging.202852] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022]
Abstract
Autophagy maintains cellular homeostasis and its dysfunction has been implicated in aging. Bats are the longest-lived mammals for their size, but the molecular mechanisms underlying their extended healthspan are not well understood. Here, drawing on >8 years of mark-recapture field studies, we report the first longitudinal analysis of autophagy regulation in bats. Mining of published population level aging blood transcriptomes (M. myotis, mouse and human) highlighted a unique increase of autophagy related transcripts with age in bats, but not in other mammals. This bat-specific increase in autophagy transcripts was recapitulated by the western blot determination of the autophagy marker, LC3II/I ratio, in skin primary fibroblasts (Myotis myotis,Pipistrellus kuhlii, mouse), that also showed an increase with age in both bat species. Further phylogenomic selection pressure analyses across eutherian mammals (n=70 taxa; 274 genes) uncovered 10 autophagy-associated genes under selective pressure in bat lineages. These molecular adaptations potentially mediate the exceptional age-related increase of autophagy signalling in bats, which may contribute to their longer healthspans.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Andrea G. Locatelli
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Present Institutional Address: Division of Genetics and Cell Biology, Fondazione Centro San Raffaele, Via Olgettina, Milano 6020132, Italy
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Carlotta Sacchi
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gavin S. Stewart
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Allio R, Scornavacca C, Nabholz B, Clamens AL, Sperling FAH, Condamine FL. Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution. Syst Biol 2019; 69:38-60. [DOI: 10.1093/sysbio/syz030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/20/2023] Open
Abstract
Abstract
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut de Biologie Computationnelle (IBC), Montpellier, France
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Anne-Laure Clamens
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Felix AH Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Fabien L Condamine
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
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