Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

Abstract

Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C. scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of C. cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of C. scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50 kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in C. scarabaeoides and C. cajan respectively. RNA editing was observed at 37 sites in both C. scarabaeoides and C. cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

Keywords: Cajanus cajan; Cajanus scarabaeoides; RNA editing; Roche 454 sequencing; chloroplast genome.

Figure 1

Map of C. scarabaeoides plastid genome. Genes shown on the outside of the map are transcribed clockwise while the genes that are shown on the inside are transcribed counterclockwise. The innermost darker gray corresponds to GC content, whereas the lighter gray corresponds to AT content. Different genes are color coded. IR, inverted repeat; LSC, large single copy region; SSC, small single copy region. Pseudogenes are marked with “^*.”

Figure 2

Map of C. cajan plastid genome. Genes shown on the outside of the map are transcribed clockwise while the genes that are shown on the inside are transcribed counterclockwise. The innermost darker gray corresponds to GC content, whereas the lighter gray corresponds to AT content. Different genes are color coded. IR, inverted repeat; LSC, large single copy region; SSC, small single copy region. Pseudogenes are marked with “^*.”

Figure 3

Gene order comparison of legume cp genomes, with Arabidopsis cp genome as reference, using MAUVE software. The boxes above the line represent the gene sequence in clockwise direction and the boxes below the line represent gene sequences in opposite orientation. The gene names at the bottom indicate the genes located at the boundaries of the boxes in cp genome of pigeonpea. AKPA1- C. scarabaeoides, AKPR375- C. cajan.

Figure 4

Sequence alignment of legume cp genomes, with C. cajan cp genome set as a reference using mVista. Position and transcriptional direction of each gene is indicated by gray arrows. Intergenic and genic regions are indicated by red and blue areas respectively. Sequence identity between the cp genomes is shown on y-axis as a percentage between 50 and 100%. AKPA1- C. scarabaeoides, AKPR375- C. cajan.

Figure 5

Comparison of the border positions of LSC, SSC, and IR regions among the legume genomes. Genes are denoted by boxes and the gaps between the genes and the boundaries are indicated by number of bases unless the gene coincides with the boundary. Extensions of the genes are also indicated above the boxes. AKPA1- C. scarabaeoides, AKPR375- C. cajan.

Figure 6

Repeat distribution among three different regions: coding sequences, intronic sequences, and intergenic spacer regions (A) AKPA1 (C. scarabaeoides); (B) AKPR375 (C. cajan).

Figure 7

SSR distribution on the basis of repeat type.

Figure 8

SSR type distribution between coding and non-coding regions (A) AKPA1 (C. scarabaeoides); (B) AKPR375 (C. cajan).