Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Pinosio, Sara; Giacomello, Stefania; Faivre-Rampant, Patricia; Taylor, Gail; Jorge, Véronique; Paslier, Marie Christine Le; Zaina, Giusi; Bastien, Catherine; Cattonaro, Federica; Marroni, Fabio; Morgante, Michèle

doi:10.1093/molbev/msw161

Cited by 95 publications

(74 citation statements)

References 73 publications

(91 reference statements)

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“…(e) Fusion transcript distribution: intra‐chromosome (purple); inter‐chromosome (yellow). The location of centromere regions is labelled according to previous research (Pinosio et al ., ).…”

Section: Resultsmentioning

confidence: 97%

The developmental dynamics of the Populus stem transcriptome

Chao

Gao

Zhang

et al. 2018

Plant Biotechnology Journal

123

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SummaryThe Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.

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Section: Resultsmentioning

confidence: 97%

The developmental dynamics of the Populus stem transcriptome

Chao

Gao

Zhang

et al. 2018

Plant Biotechnology Journal

123

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“…To determine whether levels of introgression were correlated with certain structural features of the genome, we performed a Pearson correlation (calculating coefficient r ) between admixed ancestry values and distance to telomeres. We also explored levels of introgression in predicted centromeric regions (Pinosio et al., ).…”

Section: Methodsmentioning

confidence: 99%

Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)

et al. 2018

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Introgression can introduce novel genetic variation at a faster rate than mutation alone and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expand our local ancestry analysis to the whole genome of both parents to provide a comprehensive view of introgression patterns and to identify additional candidate regions for adaptive introgression genomewide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific Northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter cold. The species hybridize where they are parapatric. We detected asymmetric patterns of introgression across the whole genome of these two poplar species adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals contained more genomic regions with unusually high levels of introgression (19 regions) and also the largest introgressed genome fragment (1.02 Mb) compared with admixed P. balsamifera (nine regions). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles in survival and adaptation. Furthermore, we detected a potential overrepresentation of subtelomeric regions in P. balsamifera introgressed into P. trichocarpa and possible protection of sex-determining regions from interspecific gene flow.

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“…As such, there is an urgent need for reference genomes in wild species, or the development of pan-genome sequences that include sequence from both wild and domesticated relatives. To characterize the pan-genome of poplar, recent work performed genome-wide analysis of structural variation in three intercrossable poplar species (Pinosio et al, 2016). Similar efforts are required in most other perennial species.…”

Section: Future Directionsmentioning

confidence: 99%

Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

2017

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Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain. Thus, MAS holds particular promise in perennials since they are often costly and time-consuming to grow to maturity and evaluate. Well-characterized germplasm that breeders can tap into for improving perennials is often limited in genetic diversity. Wild relatives are a largely untapped source of desirable traits including disease resistance, fruit quality, and rootstock characteristics. This review focuses on the use of genomics-assisted breeding in perennials, especially as it relates to the introgression of useful traits from wild relatives. The identification of genetic markers predictive of beneficial phenotypes derived from wild relatives is hampered by genomic tools designed for domesticated species that are often ill-suited for use in wild relatives. There is therefore an urgent need for better genomic resources from wild relatives. A further barrier to exploiting wild diversity through genomics is the phenotyping bottleneck: well-powered genetic mapping requires accurate and cost-effective characterization of large collections of diverse wild germplasm. While genomics will always be used in combination with traditional breeding methods, it is a powerful tool for accelerating the speed and reducing the costs of breeding while harvesting the potential of wild relatives for improving perennial crops.

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Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Cited by 95 publications

References 73 publications

The developmental dynamics of the Populus stem transcriptome

The developmental dynamics of the Populus stem transcriptome

Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)

Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

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