The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

Martin, Guillaume; Rousseau‐Gueutin, Mathieu; Cordonnier, Solenn; Lima, Oscar; Michon-Coudouel, Sophie; Naquin, Delphine; Carvalho, Julie Ferreira de; Aïnouche, Malika L.; Salmon, Armel; Aïnouche, Abdelkader

doi:10.1093/aob/mcu050

Cited by 94 publications

(133 citation statements)

References 77 publications

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“…The concatenated protein set was aligned in KAlign () and the alignment subsequently analyzed using MrBayes (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003) in the Genious platform. As expected, C. canadensis was the most closely related species to T. esculentum , with the other species following the previously determined pattern of relationships (Martin et al , 2014) in this analysis.…”

Section: Resultssupporting

confidence: 84%

A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

Kim

Cullis²

2017

Journal of Experimental Botany

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Section: Resultssupporting

confidence: 84%

A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

Kim

Cullis²

2017

Journal of Experimental Botany

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“…Molecular analysis suggested the transfer of rpl22 gene to nucleus from the cp genome, as a functional copy of this gene has been found from the nuclear genome of P. sativum (Gantt et al, 1991). Also a functional copy of rpl22 gene was verified in the nucleus of lupine species (Martin et al, 2014). The gene infA has been lost from cp genome to nucleus in the course of angiosperm evolution in almost all rosids (Millen et al, 2001).…”

Section: Resultsmentioning

confidence: 99%

“…Also it is now believed that loss of IR made the chloroplast genome more prone to rearrangements, like a 50 kb inversion reported in mung bean (Palmer and Thompson, 1982), is present in most members of the papilionoideae subfamily which changes the gene order between trnK and accD genes in the LSC region (Palmer et al, 1988). Another inversion encompassing a 78 kb region in LSC was first reported in Phaseolus and Vigna , a member of subtribe phaseolinae and tribe phaseoleae (Bruneau et al, 1990; Guo et al, 2007; Tangphatsornruang et al, 2010) and a newly reported 36 kb inversion within the 50 kb inversion present in lupines and other genisotoids (Martin et al, 2014). There seems to be variation in the legumes for the presence of certain genes.…”

Section: Introductionmentioning

confidence: 89%

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

et al. 2016

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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.

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“…Gene rps19 is nearest to the LSC-IR boundary: in some species, like I. pubescens , H. himalaica , and Panax ginseng 21, it spans the boundary, in others, like Millettia pinnata 25 and Lupinus luteus 26, it does not extend into the IR, while in others, like Phaseolus vulgaris 27, Vigna radiata 28 and Vigna unguiculata (JQ755301 in GenBank), the whole gene is inside the IR. Gene ycf1 , nearest to the SSC-IR boundary, is similar.…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genome structure in Ilex (Aquifoliaceae)

Yao

Tan

Liu

et al. 2016

Sci Rep

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Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.

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The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

Cited by 94 publications

References 77 publications

A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

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

Chloroplast genome structure in Ilex (Aquifoliaceae)

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