The Multipartite Mitochondrial Genome of Marama (Tylosema esculentum).

Jin Li,Christopher Cullis

doi:10.3389/fpls.2021.787443

Abstract

Tylosema esculentum (marama bean), a wild legume from tropical Africa, has long been considered as a potential crop for local farmers due to its rich nutritional value. Genomics research of marama is indispensable for the domestication and varietal improvement of the bean. The chloroplast genome of marama has been sequenced and assembled previously using a hybrid approach based on both Illumina and PacBio data. In this study, a similar method was used to assemble the mitochondrial genome of marama. The mitochondrial genome of the experimental individual has been confirmed to have two large circles OK638188 and OK638189, which do not recombine according to the data. However, they may be able to restructure into five smaller circles through recombination on the 4 pairs of long repeats (>1 kb). The total length of marama mitogenome is 399,572 bp. A 9,798 bp DNA fragment has been found that is homologous to the chloroplast genome of marama, accounting for 2.5% of the mitogenome. In the Fabaceae family, the mitogenome of Millettia pinnata is highly similar to marama, including for both the genes present and the total size. Some genes including cox2, rpl10, rps1, and sdh4 have been lost during the evolution of angiosperms and are absent in the mitogenomes of some legumes. However, these remain intact and functional in marama. Another set of genes, rpl2, rps2, rps7, rps11, rps13, and rps19 are either absent, or present as pseudogenes, in the mitogenome of marama.

Highlights

Tylosema esculentum, known as gemsbok bean, tamani berry, and marama bean, is a longlived perennial legume native to the Kalahari Desert and adjacent arid and semi-arid regions in Botswana, Namibia, and South Africa (Bower et al, 1988; Figure 1)
The samples were sent to the Génome Québec Innovation Centre, CWRU Genomics Core and Novogene Corporation for the Illumina sequencing and the PacBio RSII SMRT/Québec platform was used to generate the long-read sequencing data. 179,470,509 reads covering 26.9 Gb were generated from the Illumina HiSeq 2000 platform for an individual collected in Namibia and the data was used for the first round assembly due to the high coverage. 21,373,859 reads, 37,816,777 reads and 46,425,865 reads were obtained from the same Illumina platform for one individual growing at the University of Pretoria Farm and two other plants grown from seeds collected in Namibia
The Bowtie2 alignments resulted in 0.48% of the marama Illumina reads mapping to the mitochondrial genome of Millettia pinnata, 0.43% to Lotus japonicus, 0.31% to Glycine max and 0.30% to Vigna radiate

Summary

INTRODUCTION

Known as gemsbok bean, tamani berry, and marama bean, is a longlived perennial legume native to the Kalahari Desert and adjacent arid and semi-arid regions in Botswana, Namibia, and South Africa (Bower et al, 1988; Figure 1). Mitochondrial defects are associated with cytoplasmic male sterility (CMS) in plants, preventing them from producing functional pollen This can be utilized by breeders to ensure crossing of selfpollinating plants and obtain hybrid seeds (Kempken and Pring, 1999). This is one major obstacle to its cultivation and breeding, since SI reduces the yield of seeds and/or fruits for crops (Miller and Gross, 2011), and makes it extremely difficult to combine desirable traits of two incompatible parents through simple cross-pollination (Claessen et al, 2019). Plant mitochondrial genomes are very complex and diverse in size, sequence arrangement, repeat content and structure (Kubo and Mikami, 2007; Mower et al, 2012). A similar method has been used to unveil the mitochondrial genome of marama

MATERIALS AND METHODS

RESULTS AND DISCUSSION

DATA AVAILABILITY STATEMENT