1
|
Ye P, Che X, Liu Y, Zeng M, Guo W, Long Y, Liu T, Wang Z. Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine ( Pinus taeda L.). PeerJ 2024; 12:e17388. [PMID: 38799072 PMCID: PMC11122039 DOI: 10.7717/peerj.17388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.
Collapse
Affiliation(s)
- Peiqi Ye
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Xiaoliang Che
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Ming Zeng
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Wenbing Guo
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Yongbin Long
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Tianyi Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhe Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| |
Collapse
|
2
|
Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Figueroa Corona L, Allen BJ, Puiu D, Wright J, De La Torre AR, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A genome sequence for the threatened whitebark pine. G3 (BETHESDA, MD.) 2024; 14:jkae061. [PMID: 38526344 PMCID: PMC11075562 DOI: 10.1093/g3journal/jkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
Collapse
Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Whitebark Pine Ecosystem Foundation, Missoula, MT 59808, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Meltzer
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- University of California Cooperative Extension, Central Sierra, Jackson, CA 95642, USA
| | - Daniela Puiu
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jessica Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
3
|
Ousmael K, Whetten RW, Xu J, Nielsen UB, Lamour K, Hansen OK. Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach). Sci Rep 2023; 13:22488. [PMID: 38110478 PMCID: PMC10728141 DOI: 10.1038/s41598-023-49462-x] [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: 05/01/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.
Collapse
Affiliation(s)
- Kedra Ousmael
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27606, USA
| | - Jing Xu
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ulrik B Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ole K Hansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| |
Collapse
|
4
|
van Mantgem PJ, Milano ER, Dudney J, Nesmith JCB, Vandergast AG, Zald HSJ. Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California. Ecol Evol 2023; 13:e10072. [PMID: 37206686 PMCID: PMC10191741 DOI: 10.1002/ece3.10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.
Collapse
Affiliation(s)
| | - Elizabeth R. Milano
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
- Present address:
USDA Forest ServiceRocky Mountain Research StationMoscowIdahoUSA
| | - Joan Dudney
- Environmental Studies ProgramUC Santa BarbaraSanta BarbaraCaliforniaUSA
- Department of Environmental Science, Policy, & ManagementUC BerkeleyBerkeleyCaliforniaUSA
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Harold S. J. Zald
- USDA Forest ServicePacific Northwest Research StationCorvallisOregonUSA
| |
Collapse
|
5
|
Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
Collapse
Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| |
Collapse
|
6
|
Fattel L, Psaroudakis D, Yanarella CF, Chiteri KO, Dostalik HA, Joshi P, Starr DC, Vu H, Wimalanathan K, Lawrence-Dill CJ. Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. Gigascience 2022; 11:6568997. [PMID: 35426911 PMCID: PMC9012101 DOI: 10.1093/gigascience/giac023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/28/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Background Genome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes potentially responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline. Results By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain more GO terms, and are similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets across multiple species could be used together to carry out comparative functional genomics analyses in plants. To test the idea and as a proof of concept, we created dendrograms of functional relatedness based on terms assigned for all 18 genomes. These dendrograms were compared to well-established species-level evolutionary phylogenies to determine whether trees derived were in agreement with known evolutionary relationships, which they largely are. Where discrepancies were observed, we determined branch support based on jackknifing then removed individual annotation sets by genome to identify the annotation sets causing unexpected relationships. Conclusions GOMAP-derived functional annotations used together across multiple species generally retain sufficient biological signal to recover known phylogenetic relationships based on genome-wide functional similarities, indicating that comparative functional genomics across species based on GO data holds promise for generating novel hypotheses about comparative gene function and traits.
Collapse
Affiliation(s)
- Leila Fattel
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Dennis Psaroudakis
- Department of Plant Pathology and Microbiology, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Drive, Ames, Iowa 50011, USA
| | - Colleen F Yanarella
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Kevin O Chiteri
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Haley A Dostalik
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Parnal Joshi
- Department of Veterinary Microbiology and Preventive Medicine, 1800 Christensen Drive, Ames, Iowa 50011-1134, USA
| | - Dollye C Starr
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Ha Vu
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Kokulapalan Wimalanathan
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Carolyn J Lawrence-Dill
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| |
Collapse
|
7
|
Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020; 11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
Collapse
|
8
|
Weiss M, Sniezko RA, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB, De La Torre AR. Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:365-376. [PMID: 32654344 PMCID: PMC10773528 DOI: 10.1111/tpj.14928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/17/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.
Collapse
Affiliation(s)
- Matthew Weiss
- School of Forestry, Northern Arizona University, 200 E.
Pine Knoll, Flagstaff, AZ 86011
| | - Richard A. Sniezko
- Dorena Genetic Resource Center, USDA Forest Service,
Cottage-Grove, OR 97424
| | - Daniela Puiu
- Department of Biomedical Engineering, Computer Science and
Biostatistics and Center for Computational Biology, Johns Hopkins University, 3100
Wyman Park Dr., Wyman Park Building Room S220, Baltimore, MD 21211
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - Kristian Stevens
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - Steven L. Salzberg
- Department of Biomedical Engineering, Computer Science and
Biostatistics and Center for Computational Biology, Johns Hopkins University, 3100
Wyman Park Dr., Wyman Park Building Room S220, Baltimore, MD 21211
- Departments of Computer Science and Biostatistics, Johns
Hopkins University, Baltimore, MD 21218
| | - Charles H. Langley
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - David B. Neale
- Department of Plant Sciences, University of
California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E.
Pine Knoll, Flagstaff, AZ 86011
| |
Collapse
|
9
|
de María N, Guevara MÁ, Perdiguero P, Vélez MD, Cabezas JA, López‐Hinojosa M, Li Z, Díaz LM, Pizarro A, Mancha JA, Sterck L, Sánchez‐Gómez D, Miguel C, Collada C, Díaz‐Sala MC, Cervera MT. Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit-independent drought tolerance mechanisms. Ecol Evol 2020; 10:9788-9807. [PMID: 33005345 PMCID: PMC7520194 DOI: 10.1002/ece3.6613] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022] Open
Abstract
Adaptation of long-living forest trees to respond to environmental changes is essential to secure their performance under adverse conditions. Water deficit is one of the most significant stress factors determining tree growth and survival. Maritime pine (Pinus pinaster Ait.), the main source of softwood in southwestern Europe, is subjected to recurrent drought periods which, according to climate change predictions for the years to come, will progressively increase in the Mediterranean region. The mechanisms regulating pine adaptive responses to environment are still largely unknown. The aim of this work was to go a step further in understanding the molecular mechanisms underlying maritime pine response to water stress and drought tolerance at the whole plant level. A global transcriptomic profiling of roots, stems, and needles was conducted to analyze the performance of siblings showing contrasted responses to water deficit from an ad hoc designed full-sib family. Although P. pinaster is considered a recalcitrant species for vegetative propagation in adult phase, the analysis was conducted using vegetatively propagated trees exposed to two treatments: well-watered and moderate water stress. The comparative analyses led us to identify organ-specific genes, constitutively expressed as well as differentially expressed when comparing control versus water stress conditions, in drought-sensitive and drought-tolerant genotypes. Different response strategies can point out, with tolerant individuals being pre-adapted for coping with drought by constitutively expressing stress-related genes that are detected only in latter stages on sensitive individuals subjected to drought.
Collapse
Affiliation(s)
- Nuria de María
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - María Ángeles Guevara
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Pedro Perdiguero
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Centro de Investigación en Sanidad Animal (CISA‐INIA)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - María Dolores Vélez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - José Antonio Cabezas
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Miriam López‐Hinojosa
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Zhen Li
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - Luís Manuel Díaz
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Alberto Pizarro
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
| | - José Antonio Mancha
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Lieven Sterck
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - David Sánchez‐Gómez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - Célia Miguel
- BioISI‐Biosystems & Integrative Sciences InstituteFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
- Instituto de Biologia Experimental e Tecnológica (iBET)OeirasPortugal
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Grupo de investigación Sistemas Naturales e Historia ForestalUPMMadridSpain
| | | | - María Teresa Cervera
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| |
Collapse
|
10
|
Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). G3-GENES GENOMES GENETICS 2019; 9:3663-3672. [PMID: 31506321 PMCID: PMC6829139 DOI: 10.1534/g3.119.400684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.
Collapse
|
11
|
Abstract
It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor.
Collapse
|
12
|
A Reference Genome Sequence for the European Silver Fir ( Abies alba Mill.): A Community-Generated Genomic Resource. G3-GENES GENOMES GENETICS 2019; 9:2039-2049. [PMID: 31217262 PMCID: PMC6643874 DOI: 10.1534/g3.119.400083] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species’ future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.
Collapse
|
13
|
Lu FH, McKenzie N, Kettleborough G, Heavens D, Clark MD, Bevan MW. Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries. Gigascience 2018; 7:4995264. [PMID: 29762659 PMCID: PMC5967450 DOI: 10.1093/gigascience/giy053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/04/2018] [Indexed: 12/20/2022] Open
Abstract
Background The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Results Here we use a Fosill 38-kb jumping library to assess medium and longer–range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Conclusions Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.
Collapse
Affiliation(s)
- Fu-Hao Lu
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neil McKenzie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Darren Heavens
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Matthew D Clark
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Michael W Bevan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
14
|
Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dalgard CL, Sarkar S, Schnable PS. Linked read technology for assembling large complex and polyploid genomes. BMC Genomics 2018; 19:651. [PMID: 30180802 PMCID: PMC6122573 DOI: 10.1186/s12864-018-5040-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/27/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. RESULTS Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~ 172,000 scaffolds with an N50 of 89 kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with > 76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~ 83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. CONCLUSIONS Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes.
Collapse
Affiliation(s)
- Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- Present address: Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI 53719 USA
| | - James C. Schnable
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
- Data2Bio LLC, 2079 Roy J Carver Co-Laboratory, 1111 WOI Rd, Ames, IA 50011 USA
- Dryland Genetics LLC, 2073 Roy J Carver Co-Laboratory, 1111 WOI Rd, Ames, IA 50011 USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- Data2Bio LLC, 2079 Roy J Carver Co-Laboratory, 1111 WOI Rd, Ames, IA 50011 USA
| | - Linjiang Wu
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - Chao Liu
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
- Present address: Department of Thermal Engineering, Tsinghua University, Beijing, 100084 China
| | - Heng-Cheng Hu
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Present address: Qiagen Sciences Inc, 6951 Executive Way, Frederick, MD 21703 USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- Data2Bio LLC, 2079 Roy J Carver Co-Laboratory, 1111 WOI Rd, Ames, IA 50011 USA
- Dryland Genetics LLC, 2073 Roy J Carver Co-Laboratory, 1111 WOI Rd, Ames, IA 50011 USA
| |
Collapse
|
15
|
Abstract
Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.
Collapse
|