Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding

Abstract

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.

Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

“…The N50 contig length is 3,850 bp (when considering contigs > 1,000 bp). The six largest scaffolds represent the largest chloroplast or mitochondrial scaffolds as determined by BlastN analysis (data not shown) versus the genomic sequences of both organelles (Kersten et al, 2016).…”

“…The draft genomic scaffolds of INRA 717-1B4 created in this study supplement the existing genomic sequence resources for this clone, namely the "sPta717 Genome" described in the Introduction and the complete DNA sequences of the chloroplast and the mitochondrial genomes which we published recently (Kersten et al, 2016). In contrast to the "sPta717 Genome", our new resource provides also access to sequences of INRA 717-1B4 in genomic regions that show no or only a low similarity to the P. trichocarpa reference genome.…”

Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

“…Additionally, promising indels have been found beside SNPs in the same investigations in four chloroplast regions (psbA_matK, rps4_trnL, rps2_rpoC2, and trnC_petN). In a previous paper, we aligned whole plastome sequences of eight poplar species (P. tremula, P. alba, P. trichocarpa, P. balsamifera, P. euphratica, P. cathayana, P. fremontii, and P. yunnanensis) and looked in the first line for long indels [18]. One of the cp regions examined there, psaA_ycf 13, was very promising because of a high number of polymorphisms, and has therefore been included as a new region to be tried in the present study.…”

“…These nine chloroplast regions were tested in a total of 19 poplar species, partly with the already published primers, and partly with newly designed primers, as given in Table 1. Based on the above-mentioned whole plastome alignment [18], a very long indel was identified in the region psbE_petL that was further investigated with up to 18 poplar species in this study.…”

“…Within the region psbE_petL resulting from the whole cp genome alignment [18], a large indel of 99 bp was identified, where P. tremula was 99 bp shorter than the other species. The indel has been validated with one to three individuals per species for 17 of the 19 species (P. grandidentata and P. fremontii were not included), and with an additional 14 P. tremula specimens simply on an agarose gel.…”