Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato.

The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B1 subgenome, IbT-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B2 subgenome, IbT-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B1 to B2 subgenome conversions was nearly three times higher than that of B2 to B1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop.

The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato.

The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species.

Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs.

Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals. In plants, one well-studied example of HGT is the transfer of the tumor-inducing genes (T-DNAs) from some Agrobacterium species into their host plant genomes. Evidence of T-DNAs from Agrobacterium spp. into plant genomes, and their subsequent maintenance in the germline, has been reported in Nicotiana, Linaria and, more recently, in Ipomoea species. The transferred genes do not produce the usual disease phenotype, and appear to have a role in evolution of these plants. In this paper, we review previous reported cases of HGT from Agrobacterium, including the transfer of T-DNA regions from Agrobacterium spp. to the sweetpotato [Ipomoea batatas (L.) Lam.] genome which is, to date, the sole documented example of a naturally-occurring incidence of HGT from Agrobacterium to a domesticated crop plant. We also discuss the possible evolutionary impact of T-DNA acquisition on plants.

Importancia de la RT-PCR Cualitativa en la evidencia directa de la viremia activa del virus de la hepatitis C / Importance of the Qualitative RT-PCR in the direct evidence of viremia activates of the virus of hepatitis C

El virus de la Hepatitis C (VHC), asociado a cronicidad y a carcinoma hepatocelular (CHC), es la mayor causa de hepatitis parenteral no-A, no-B. La infección por VHC es usualmente diagnosticada por pruebas que detectan anticuerpos circulantes para antígenos VHC, reflejando la respuesta inmune sin indicar la viremia activa. Objetivo: detectar viremia activa del VHC, en individuos con o sin antecedentes de exposición a factores de riesgo conocidos (EFRC), empleando la reacción en cadena de la polimerasa cualitativa (RT-PCRc). Material y Método: se estudiaron seis muestras de sangre periférica, de individuos con EFRC y 6 sin EFRC. Se extrajo ARN de cada muestra la cual fue sometida a síntesis de ADNc y posterior amplificación in vitro de un segmento génico viral-VHC con RT-PCRc. Resultado: En 5/6 (83.3 por ciento) casos con EFRC se detectó viremia, 2/5 de ellos fueron sero-negativos. En 2/6 (33.3 por ciento) casos sero negativos sin EFRC la RT-PCRc fue positiva para ARN - VHC. Conclusión: la sensibilidad de la prueba molecular cualitativa nos permitió detectar en individuos sero-positivos y sero-negativos con EFRC a aquellos con viremia activa e identificar en aquellos sin EFRC y serología negativa a individuos con infección oculta, portadores asintomáticos, aparentemente sanos.