BR De Marchi , T Kinene, R Krause-Sakate, LM Boykin, J Ndunguru, M Kehoe, E Ateka, F Tairo, J Amisse, P Sseruwagi

PeerJ. 2020 Mar 2;8:e8632.  doi: 10.7717/peerj.8632.

Abstract

Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.

See https://pubmed.ncbi.nlm.nih.gov/32175188/

Figure 1: Phylogenetic relationships among cassava chloroplast coding regions collected in East Africa.

The cassava plants were clustered in three main clades (A–C). The viruses detected on the samples are indicated in colorful letters inside gray squares: Ugandan cassava brown streak virus (UCBSV), Cassava brown streak virus (CBSV), East African cassava mosaic virus (EACMV-Ug) and East African cassava mosaic Zanzibar virus (EACMZV). Samples obtained from GenBank are highlighted in blue.

Illumina sequencing of libraries prepared from total DNA produced between 2,071,164 and 23,427,360 paired-end reads with a maximum sequence length of 100 nucleotides and minimum of 30 nucleotides for Kenyan samples, maximum sequence length of 300 nucleotides and minimum of 100 nucleotides for Tanzanian samples, maximum of 300 and minimum of 100 nucleotide sequence length for the Mozambican samples.

The phylogeny reconstruction consisted of an 35,439 bp alignment and included 55 protein-coding genes for a dataset with 39 taxa. The single-copy genes analyzed (53 genes) were psbA,  atpA,  atpF,  atpH,  atpI,  rps2,  rpoC1,  psbM,  psbD,  psbC,  psbZ,  rps14,  psaB,  psaA,  ycf3,  rps4,  ndhJ,  ndhK,  ndhC,  atpE,  atpB,  rbcL,  psaI,  ycf4,  cemA,  petA,  psbJ,  psbL,  psbF,  psbE,  petG,  psaJ,  rpl33,  rpl20,  clpP,  psbB,  psbT,  psbN,  psbH,  petB,  rps11,  rpl36,  rps8,  rpl14,  rpl16,  rps3,  rpl22,  psaC,  ndhE,  ndhG,  ndhI,  ndhA and ndhH. The genes duplicated in the IR analyzed (2 genes) were rps7 and rpl23. All the GenBank Accessions from the nucleotide sequences obtained in this study are available.