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Plant Organelle Genome Replication
Open AccessArticle

De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales)

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Laboratorio de Ecología Molecular y Evolución, UBIPRO, FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Estado de México, Mexico
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Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, Cuernavaca 62250, Mexico
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Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, FES Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Estado de México, Mexico
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Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua carretera a Pátzcuaro 8701, Ex-Hacienda San José La Huerta, Morelia 58190, Michoacán, Mexico
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Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 04510, Mexico
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Laboratorio de Recursos Naturales, UBIPRO, FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Estado de México, Mexico
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Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
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Authors to whom correspondence should be addressed.
Plants 2019, 8(10), 392; https://doi.org/10.3390/plants8100392
Received: 21 August 2019 / Revised: 20 September 2019 / Accepted: 22 September 2019 / Published: 1 October 2019
(This article belongs to the Special Issue Plant Organelle DNA Maintenance)
The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages. View Full-Text
Keywords: divergent inverted repeats; short-globose cacti; novel gene rearrangements; pseudogenization divergent inverted repeats; short-globose cacti; novel gene rearrangements; pseudogenization
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Solórzano, S.; Chincoya, D.A.; Sanchez-Flores, A.; Estrada, K.; Díaz-Velásquez, C.E.; González-Rodríguez, A.; Vaca-Paniagua, F.; Dávila, P.; Arias, S. De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales). Plants 2019, 8, 392.

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