Peanut is a crop of the Kayabi tribe, inhabiting the Xingu Indigenous Park, Brazil. Morphological analysis of Xingu accessions showed variation exceeding that described for cultivated peanuts. This raised questions as to the origin of the Xingu accessions: are they derived from different species, or is their diversity a result of different evolutionary and selection processes? To answer these questions, cytogenetic and genotyping analyses were conducted. The karyotypes of Xingu accessions analyzed are very similar to each other, to an A. hypogaea subsp. fastigiata accession and to the wild allotetraploid A. monticola. The accessions share the number and general morphology of the chromosomes; DAPI + bands; 5S and 45S rDNA loci distribution and a high genomic affinity with A. duranensis and A. ipaënsis genomic probes. However, the number of CMA 3 + bands differs from those determined for A. hypogaea and A. monticola, which are also different from each other. SNP genotyping grouped all Arachis allotetraploids into four taxonomic groups: Xingu accessions were closer to A. monticola and A. hypogaea subsp. hypogaea. Our data suggests that the morphological diversity within these accessions is not associated with a different origin and can be attributed to morphological plasticity and different selection by the Indian tribes.

Background, Leucoptera coffeella (Guerin-Meneville, 1842) is a moth species (Lyonetiidae, Lepidoptera) pest that causes severe losses to coffee crops. Further information about its genomic data is required to allow molecular strategies for the development of sustainable pesticides and to gain in-depth knowledge on phylogenetics. However, the closest complete genome available is within the superfamily level (Yponomeutoidea). Here we report the generation of the first long-read genome, transcriptome and proteome results of L. coffeella and the in silico analysis performed in these molecular levels to investigate genes involved in the siRNA processing. Results, PACBio and paired-end Illumina combined DNA sequencing from pupae samples resulted in more than 436 Gb subreads and 31Mb reads with N50 read length of 15,512 nt, mean read length 13.8 Kb and max read length 420.7 Kb. Additionally, 20Gb data of short DNA sequencing was combined to produce 1,984 contigs comprising 397 Mb in total. The longest and shortest scaffold sizes are 10,809,567 nt and 15,247 nt, respectively (mean size 200,178 nt). The N50 scaffold was 275,598 nt and the GC content was 36.10%. Predicted coding DNA sequences counted 39.930 gene models. Searching of 5286 BUSCO groups revealed 91.7 percent of completeness (single and duplicated genes combined) compared to lepidoptera genomes (lepidoptera_odb10). Flow cytometry showed the 1C DNA content is approximately 295 Mb. RNA-Seq from seven development stages resulted in 28294 identified transcripts. Additionally, proteomics from immature stages resulted in 2045 proteins matching the gene models. Conclusions, This first nuclear genome of the Lyonetiidae family brings valuable molecular resources to study Lepidoptera genomes. Genome, transcriptome and proteome sequencing to raise genome annotation precision may resolve uncovered taxonomic issues. In addition, these combined approaches provide insights into plant-insect interaction players, as horizontally transferred genes (HGT) and endosymbionts. Put together, the generated data enables the development of molecular tools towards sustainable biotechnology solutions for lepidopteran pest control.

There is a strong demand for sustainable, durable, safe, and specific solutions against agricultural pests due to breeding limitations and chemical control constraints. Biotechnological approaches to insect pests require phylogenetic information at the molecular level for RNAi application and other tailored strategies, such as insecticide resistance molecular markers. Sequencing technologies have advanced in resolution, speed, and cost-effectiveness to offer striking impact on genomics and transcriptomics. To provide deep and reliable data to high-throughput studies, state-of-the art technologies require high purification and integrity of the submitted samples. However, the limited number of existing protocols to obtain high mass nucleic acids from insects render difficult to obtain elevated purity and integrity standards. Species characteristics, as scales covered bodies of Lepidoptera and mining eating habits, hinder the quality of nucleic acid samples. Additionally, small size individuals are limited to yield sufficient amounts to robust base sequence coverage. The coffee leaf miner (CLM) Leucoptera coffeella is microlepdoptera insect responsible for severe leaf damage and huge yield losses to the coffee crop. Here we present simple and reproducible procedures we used to successfully obtain the whole-genome long-read PACBIO and Illumina (DNA) and transcriptome (RNA) of L. coffeella for de novo assembly. Therefore, we developed customized protocols applicable to insects to the extraction of genomic High Molecular Weight DNA and total RNA suitable for downstream high standard sequencing applications and other sensitive molecular analyses.

Distribuição de retrotansposons do tipo LTR e sequências de DNA ribossômico em cromossomos de genótipos diploides e tetraploides de Arachis spp. por hibridização in situ por fluorescência -FISH