Complete Chloroplast Genome Sequence of Glycine max and Comparative Analyses with other Legume Genomes

Abstract

Lack of complete chloroplast genome sequences is still one of the major limitations to extending chloroplast genetic engineering technology to useful crops. Therefore, we sequenced the soybean chloroplast genome and compared it to the other completely sequenced legumes, Lotus and Medicago. The chloroplast genome of Glycine is 152,218 basepairs (bp) in length, including a pair of inverted repeats of 25,574 bp of identical sequence separated by a small single copy region of 17,895 bp and a large single copy region of 83,175 bp. The genome contains 111 unique genes, and 19 of these are duplicated in the inverted repeat (IR). Comparisons of Glycine, Lotus and Medicago confirm the organization of legume chloroplast genomes based on previous studies. Gene content of the three legumes is nearly identical. The rpl22 gene is missing from all three legumes, and Medicago is missing rps16 and one copy of the IR. Gene order in Glycine, Lotus, and Medicago differs from the usual gene order for angiosperm chloroplast genomes by the presence of a single, large inversion of 51 kilobases (kb). Detailed analyses of repeated sequences indicate that many of the Glycine repeats that are located in the intergenic spacer regions and introns occur in the same location in the other legumes and in Arabidopsis, suggesting that they may play some functional role. The presence of small repeats of psbA and rbcL in legumes that have lost one copy of the IR indicate that this loss has only occurred once during the evolutionary history of legumes.

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

“…Gene order in chickpea is similar to the ancestral angiosperm gene order except for the loss of one copy of the IR and by the presence of a single, large inversion of approximately 50 kb that reverses the order of the genes between rbcL and rps16. The same inversion is present in the four other completely sequenced legume plastid genomes Glycine max (Saski et al, 2005), Lotus japonicus (Kato et al, 2000), Medicago truncatula, and Phaseolus vulgaris (Guo et al, 2007), and is apparently shared by the majority of papilionoid legumes (Doyle et al, 1996). The AT content of the chickpea plastid genome is 66.1%, similar to other legumes including Glycine max (64.63%), Lotus japonicus (64.0%), Phaseolus vulgaris (64.56%), and Medicago truncatula (66.03%).…”

“…MultiPipMaker (Schwartz et al, 2003; http://bio.cse.psu.edu) was used for multiple genome alignment of chickpea with four published legume plastid genomes from the subfamily Papilionoideae; Lotus japonicus (NC_002694, Kato et al, 2000), Medicago truncatula (NC_003119), Glycine max (NC_007942, Saski et al, 2005), and Phaseolus vulgaris (NC_009259, Guo et al, 2007). We generated the alignments of whole genomes using chickpea as the reference genome.…”

“…However, complete chloroplast genome sequence of only six species of crop plants were determined until 2004. Therefore, complete plastid genome sequences of several major crop species including fiber crops , tubers (Daniell et al, , 2008, cereals (Saski et al, 2007), trees (Steane, 2005;Bausher et al, 2006;Ravi et al, 2006;Samson et al, 2007), vegetables (Ruhlman et al, 2006), fruits Daniell et al, 2006) and legumes (Saski et al, 2005;Guo et al, 2007) have been determined recently. Plastid genetic engineering offers a number of unique advantages including high level of transgene expression (DeCosa et al, 2001), multi-gene engineering in a single transformation event (Quesda-Vargas et al, 2005), transgene containment via maternal inheritance (Daniell, 2002;Daniell, 2007) or cytoplasmic male sterility .…”

“…In wheat (Ogihara et al, 1988) and Oenothera (Hupfer et al, 2000), such repeats have been directly implicated in inversions, and the strong correlation detected between the number of dispersed repeats and the extent of genomic rearrangements in several lineages is consistent with this explanation (Pombert et al, 2005(Pombert et al, , 2006Haberle et al, 2008). Recent comparisons of the number and distribution of repeated sequences in completely sequenced legume plastid genomes have demonstrated the presence of numerous dispersed repeats, many more than in related rosid genomes that are not rearranged (Saski et al, 2005).…”

Extremely high cytoplasmic diversity in natural and breeding populations of Lolium (Poaceae)

“…Furthermore, detailed characterization of plastid type is essential in studies investigating nucleo-cytoplasmic effects (Hallden et al, 1993), since plastid signals controlling nuclear gene expression can have both positive and negative effects on gene expression (Gray, 2005). Several chloroplast genes may have importance for genetic engineering such as those involved in synthesis of fatty acids, amino acids and vitamins (Saski et al, 2005) or for the directed manipulation of plant lines in breeding programmes . Worldwide breeding efforts for the improvement of L. perenne and its allies are ongoing and depend upon well-characterized genetic resource collections.…”