Genómica de poblaciones y genética del paisaje de la abeja melífera ibérica (Apis mellifera iberiensis)

Estudia los complejos patrones de variación de la abeja ibérica (Apis mellifera iberiensis) de la zona híbrida que utiliza el ARNt altamente polimórfico mitocondrial leu-cox2, polimorfismos de nucleótido único (SNP) de la región y del genoma nuclear. Analiza un marcador PCR-RFLP, conocido como prueba DraI, en el tRNAleu-cox2 región intergénica de colonias muestreadas en Portugal. Usando esta prueba, 16 nuevos haplotipos se identificó de la ascendencia africana, 15 pertenecientes al sublinaje AIII y 1 al sublinaje AI. El resultado sugiere que el lado atlántico de la Península Ibérica es un importante reservorio de diversidad que se ha pasado por alto debido al submuestreo en estudios anteriores.Portugal. Fundación para la Ciencia y Tecnología - FCT: Beca de DoctoradoTesi

Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis)

Tese de Doutoramento em Biologia Molecular e Ambiental - Especialidade em Evolução, Biodiversidade e EcologiaThe goal of this study was to disentangle the complex variation patterns of the Iberian honey bee ( Apis mellifera iberiensis) hybrid zone using the highly polymorphic tRNAleu-cox2 mitochondrial region and nuclear genome-wide Single Nucleotide Polymorphisms (SNPs). Initially, a maternal analysis was performed using a PCR-RFLP marker, known as the DraI test, in the tRNAleu-cox2 intergenic region of colonies sampled in Portugal (N=950). Using this test, 16 novel haplotypes of African ancestry, 15 belonging to sub-lineage AIII and 1 to sub-lineage AI, were identified. This result suggests that the Atlantic side of the Iberian Peninsula is an important reservoir of maternal diversity that has been missed out because of under-sampling in previous studies. To obtain a fuller picture of maternal diversity patterns in the Iberian honey bee, 711 drones, sampled across three north-south Iberian transects, were screened for tRNAleu-cox2 variation using sequence data. The tRNAleu-cox2 sequence revealed a more complex diversity pattern of haplotypes in the Iberian honey bee than previously thought when using only the DraI test, which is reflected by detection of 164 novel haplotypes of African (lineage A) and Western European (lineage M) ancestry. At the same time, the distribution of haplotypes A and M reported in this study has further refined the well-defined Southwestern-Northeastern clinal pattern previously described, and also has rescued and reinforced the hypothesis of a hybrid origin for the Iberian honey bee. The distribution pattern of both lineages suggests the presence of two glacial refuges located in the Northeastern and Southern of Iberia. Nonetheless, the confined distribution of sub-lineage AIII to the North Atlantic side of Iberia suggests a putative third refuge, an hypothesis that deserves further investigation. A phylogenetic tree representing over 281 haplotypes, of which 8 exhibited intermediate A and M characteristics, resolved that the AI, AII, AIII cluster and lineage M are sister groups, which have probably diverged from a common ancestor similar to sub-lineage Z. These findings suggest that lineage M might have a more ancestral African origin, not from North African populations but from Northeastern African and Near East populations where haplotypes of sub-lineage Z have been reported. The low number of colonies (only 1) carrying haplotypes of Eastern European ancestry (lineage C) indicates that importation of commercial honey bees is residual in Iberia, which contrasts with other regions of Western Europe where C-lineage honey bees are replacing the native subspecies. Analysis of selection was carried out to find out if this evolutionary force has been shaping the complex patterns of Iberian honey bees. The 711 drones were screened for 1536 SNPs using the GoldenGate Assay of Illumina, of which only 383 revealed polymorphic. While a total of 69 outlier SNPs were identified using two coalescent and two Bayesian methods, only 17 were crossvalidated by the four methods. Additionally, a spatial method identified 33 outlier SNPs of which 28 coincided with the previous four methods. Among the 17 outliers, 10 exhibited the strongest signal of selection (9 directional and 1 balancing). 71 outlier SNPs were located in or near genes involved in putative functions as signaling, structural, metabolism, regulation, transport, and immunity. Vision, xenobiotic detoxification and immune response mechanisms were well represented by several genes under selection. For the vision mechanism, five genes are responsible for neural development, synapse formation, axon guidance, regeneration and production of chromophore (formation of rhodopsin). For xenobiotic detoxification, three genes are responsible for tolerance to plant toxins and insecticide resistance. Finally, the two genes related with innate immune response participate in the phagocytosis process. The spatial analysis corroborated that selection is an underlying force shaping a latitudinal and longitudinal gradient. Population structure was inferred from both maternal (tRNAleu-cox2 intergenic region) and biparental (SNPs) markers using spatial and non-spatial methods. The geographical distribution of lineages A and M revealed a sharp southwestern-northeastern maternal cline. Congruent with the mtDNA, population structure inferred from SNPs indicates the presence of two clusters that remarkably overlap the distribution of A and M maternal lineages. These results support a process of secondary contact between divergent honey bee populations in Iberia. Further support for the secondary contact hypothesis comes from (i) geographic cline analysis, which revealed the existence of multiple coincident clines, (ii) elevated values of linkage disequilibrium and of diversity towards the center of the cline. The previous findings suggest the existence of two putative refuges located in Northeastern (between Iberian Mountain Range and Pyrenees) and Southern (Betic Ranges in Spain) Iberia, as proposed for a growing list of other Iberian taxa. In summary, the complex diversity patterns exhibited by Iberian honey bees has seemingly been shaped by a process of secondary contact between two highly divergent groups (A and M), together with selective forces producing local adaptation to a very heterogeneous area as the Iberian Peninsula.O objectivo deste estudo é a compreensão dos padrões de variação da abelha ibérica ( Apis mellifera iberiensis), usando uma região mitocondrial altamente polimórfica e os polimorfismos de nucleótido únicos (SNPs) localizados ao longo do genoma nuclear. Inicialmente foi efectuada uma análise dos marcadores maternos em colónias amostradas em Portugal (N=950) para isso usou-se PCR-RFLP, conhecido por teste DraI, na região intergénica tRNAleu-cox2. Usando este teste, 16 novos haplótipos foram identificados com ancestralidade Africana, 15 pertencentes à sub-linhagem AIII e 1 à sub-linhagem AI. Estes resultados sugerem que o lado Atlântico da Península Ibérica é um reservatório importante da diversidade materna, que ficou negligenciado devido à amostragem efectuada pelos estudos anteriores não incorporar esta região geográfica. Para obter um panorama completo dos padrões de diversidade materna da abelha ibérica, 711 machos amostrados em três transectos norte-sul ao longo da Península Ibérica, foram estudados usando a variação da sequência da região intergénica tRNAleu-cox2. A sequência tRNAleucox2 revelou um padrão de diversidade de haplótipos mais complexo do que o que anteriormente se tinha verificado quando se usou apenas o teste DraI, aqui observou-se a presença de 164 haplótipos novos de ancestralidade Africana (linhagem A) e da Europa Ocidental (linhagem M). Ao mesmo tempo, a distribuição dos haplótipos A e M reportado neste estudo refinou o cline bem definido Sudoeste-Nordeste, o que resgatou e reforçou a hipótese de uma origem híbrida das abelhas ibéricas. A distribuição do padrão das duas linhagens sugere a presença de dois refúgios glaciares localizados no Nordeste e Sul da Ibéria. Não obstante, a distribuição confinada da sublinhagem AIII no lado Atlântico Norte da Ibéria sugere um terceiro refúgio potencial, uma hipótese que necessita de estudos adicionais. A árvore filogenética onde se encontram mais de 281 haplótipos, 8 dos quais mostram características intermédias entre a linhagem A e M, mostra que o grupo AI, AII, AIII e a linhagem M são grupos irmãos, que provavelmente divergiram de um ancestral comum com características similares à sub-linhagem Z. Estes dados sugerem que a linhagem M pode ter uma origem Africana mais ancestral, não do Norte de África mas sim de populações do Nordeste Africano e Médio Oriente onde os haplótipos de sub-linhagem Z têm sido reportados. O baixo número de colónias (apenas uma) que mostram haplótipos de ancestralidade do leste Europeu (linhagem C) indicam que a importação de abelhas comerciais na Península Ibérica é residual, comparado com outras regiões da Europa Ocidental, onde as abelhas de linhagem C têm vindo a substituir as abelhas locais. Foram efectuadas análises de selecção para perceber se esta força evolutiva tem vindo a moldar os padrões complexos da abelha ibérica. Os 711 machos foram genotipados para 1536 SNPs usando GoldenGate Assay da Illumina, dos quais apenas 383 eram polimórficos. O total de 69 SNPs foram detectados usando dois métodos coalescente e dois métodos Bayesianos, apenas 17 foram detectados pelos quatro métodos. Adicionalmente, um método espacial identificou 33 SNPs outliers, 28 dos quais coincidem com os quatro métodos prévios. Entre os 17 outliers, 10 mostram um sinal de selecção muito forte (9 direccionais e 1 balanceadora). 71 SNPs outliers estão localizados dentro ou perto de genes, tendo como funções putativas a sinalização, estrutura, metabolismo, regulação, transporte e imunidade. Mecanismos de visão, destoxificação xenobiótica e resposta imune estiveram bem representados por vários genes que mostram SNPs com sinais de selecção. Para o mecanismo da visão, 5 genes são responsáveis pelo desenvolvimento neuronal, formação de sinapses, orientação de axónios, regeneração e produção do cromóforo (formação da rodopsina). Para a destoxificação xenobiótica, três genes são responsáveis pela tolerância a toxinas de plantas e resistência a insecticida. Finalmente, dois genes relacionados com a resposta imune inata, participam no processo de fagocitose. As análises espaciais corroboram que a selecção é uma força que molda o gradiente latitudinal e longitudinal. A estrutura populacional foi inferida tanto por marcadores maternos (região intergénica tRNAleu-cox2) como por biparentais (SNPs) usando métodos espaciais e não-espaciais. A distribuição geográfica das linhagens A e M revelam um cline materno sudoeste-nordeste bem definido. Concordante com o ADNmt, a estrutura populacional inferida pelos SNPs indica a presença de dois grupos, que sobrepões com a distribuição das linhagens maternas A e M. Estes resultados suportam o processo de contacto secundário entre duas populações divergentes de abelhas na Ibéria. Outra evidencias que suportam a hipótese de contacto secundários advém (i) da análise do clino geográfico, que revela a existência de múltiplos clinos coincidentes, (ii) valores elevados de linkage disequilibrium e diversidade em direcção ao centro do clino. Estudos prévios sugerem a existência de refúgios potenciais localizados no Nordeste da Ibéria (entre o Sistema Ibérico e os Pireneus) e o no Sul (Sistema Bético em Espanha), tal como sugerido para um número crescente de taxa ibéricos. Em suma, os padrões complexos de diversidade apresentados pela abelha ibérica, parecem ter sido moldados por processos de contacto secundário de dois grupos divergentes (A e M), juntamente com as forças selectivas que levaram à adaptação local a uma área muito heterogénea como a Península Ibérica.El objetivo de este estudio fue desenmarañar los padrones complejos de variación de la zona híbrida de la abeja ibérica ( Apis mellifera iberiensis) usando la región mitocondrial altamente polimórfica tRNAleu-cox2 y polimorfismos de nucleótido simples (SNPs) nucleares del todo el genoma. Inicialmente, un análisis maternal fue llevado a cabo usando un marcador PCR-RFLP, conocido como el test DraI, en la región intergénica de colonias muestreadas en Portugal (N=950). Usando este test, 16 nuevos haplótipos de origen Africano, 15 pertenecientes al sub-linaje AIII y 1 a sub-linaje AI fueron identificados. Este resultado sugiere que el lado Atlántico de la Península Ibérica es un importante reservorio de diversidad maternal que ha sido omitido en previos estudios por causa de un muestreo más amplio. Para obtener una imagen complete de padrones de diversidad materna en la abeja ibérica, 711 machos, muestreados a través de tres transectos norte-sur a lo largo de la Península Ibérica, fueron analizados para la variación de la secuencia de tRNAleu-cox2. La secuencia de esta región presentó una mayor complejidad de padrón de diversidad de haplótipos en la abeja ibérica de lo que se había pensado cuando usando el test DraI, lo cual es reflejado en la detección de 164 nuevos haplótipos de origen Africano (linaje A) y Europeo Occidental (linaje M). Al mismo tiempo, la distribución de haplótipos A y M reportados en este estudio, ha extra refinado el bien definido padrón clinal Suroeste- Nordeste previamente descrito, y también ha rescatado y reforzado la hipótesis del origen híbrido de la abeja ibérica. El padrón de distribución de ambos linajes sugiere la presencia de dos refugios glaciares localizados en el Nordeste y Sur de Iberia. No obstante, la distribución confinada del sub-linaje AIII al lado Nord Atlántico de Iberia sugiere un putativo tercer refugio, una hipótesis que merece extra investigación. Un árbol filogenético inferido de 281 haplótipos, donde 8 haplótipos exhibieron características intermedias de los linajes A y M, resolvió que el grupo AI, AII, AIII y linaje M son grupos hermanos, los cuales probablemente han divergido de un común ancestro similar al sub-linaje Z. Estos hallazgos sugieren que el linaje M podría tener un origen más antiguo, no de poblaciones Nord Africanas sino de poblaciones Nord-Orientales Africanas y de Medio Oriente donde haplótipos del sub-linaje Z han sido reportados. El bajo número de colonias presentando haplótipos de origen Europeo Oriental (linaje C) indica que la importación de abejas comerciales es residual en Iberia, lo cual contrasta con otras regiones de Europa Occidental donde abejas de linaje C están reemplazando a las subespecies nativas. Análisis de selección fue realizado para averiguar si esta fuerza evolucionaria ha estado formando los padrones complejos de la abeja ibérica. Los 711 machos fueron analizados para 1536 SNPs usando GoldenGate Assay de Illumina, de los cuales solo 383 revelaron polimorfismo. Mientras un total de 69 SNP outliers fueron identificados usando dos métodos de coalescencia y dos métodos bayesianos, solo 17 fueron por los cuatro métodos. Adicionalmente, un método espacial identificó 33 SNP outliers de los cuales 28 coincidieron con los cuatro métodos anteriores. Entre los 17 outliers, 10 exhibieron las más fuertes señales de selección (9 direccionales y 1 balanceadora). 71 SNPs outliers fueron localizados dentro o cerca de genes involucrados en funciones putativas como señalización, estructural, metabolismo, regulación transporte, e inmunidad. Mecanismos de visión, detoxificación xenobiótica y respuesta inmune estuvieron bien representados por varios genes bajo selección. Para el mecanismo de la visión, cinco genes son responsables para desenvolvimiento neural, formación de sinapsis, orientación del axón, regeneración y producción del cromóforo (formación de rodopsina). Para la detoxificación xenobiótica, tres genes son responsables para la tolerancia a toxinas de plantas y resistencia a insecticidas. Finalmente, los dos genes relacionados con la respuesta inmune innata participan en el proceso de fagocitosis. El análisis espacial corroboró que la selección es una fuerza fundamental formando un gradiente latitudinal y longitudinal. La estructura poblacional fue inferida tanto del marcador materno (región intergénica tRNAleu-cox2) como de biparentales (SNPs) usando métodos espaciales y no espaciales. La distribución geográfica de linajes A y M reveló un marcado clino materno Suroeste- Nordeste. Congruente con el ADNmt, la estructura poblacional inferida de SNPs indica la presencia de dos grupos que extraordinariamente se sobreponen a la distribución de los linajes A y M. Estos resultados soportan un proceso de contacto secundario entre poblaciones divergentes de abejas en Iberia. Otras evidencias que soportan la hipótesis de contacto secundario viene de (i) análisis de clinos geográficos, los cuales revelaron la existencia de multiple clinos coincidentes, (ii) valores elevados de linkage disequilibrium y de diversidad hacia el centro del clino. Los hallazgos anteriores sugieren la existencia de dos putativos refugios localizados en el Nordeste (entre las Sistema Ibérico y Pirineos) y el Sur de Iberia (Sistemas Béticos en España), como propuesto para una lista creciente de otros taxa ibéricos. En resumen, los complejos padrones de diversidad exhibidos por la abeja ibérica ha sido aparentemente formado por un proceso de contacto secundario entre dos grupos altamente divergentes (A y M), junto con fuerzas selectivas produciendo adaptación local en un área muy heterogénea como la Península Ibérica.Le but de cette étude était de comprendre les variations complexes qui façonnent la diversité de l’abeille mellifère ibérique ( Apis mellifera iberiensis) au sein d’une zone hybride utilisant la région mitochondrial particulièrement polymorphe -tRNAleu-cox2- et le polymorphisme d’un seul nucléotide (SNPs). Une analyse des fragments de restriction (PCR-RFLP) de la région intergénique mitochondriale tRNAleu-cox2, connue sous le nom de test DraI a tout d’abord permis de déterminer l’origine maternelle des colonies échantillonnées au Portugal (N=950). 16 nouveaux haplotypes d’origine africaine ont été identifiés parmi lesquels 15 appartiennent à la sous-lignée évolutive AIII et 1 à la sous-lignée évolutive AI. Ces résultats suggèrent que la côte Atlantique de la Péninsule Ibérique comporte une importante diversité mitochondriale, ce qui, par manque d’échantillonnage, n’avait pas été décrit dans les études précédentes. Afin d’obtenir un aperçu plus exhaustif de la diversité mitochondriale présente chez l’abeille ibérique, la région intergénique tRNAleu-cox2 a été séquencée pour 711 faux-bourdons échantillonnés le long de trois gradients Nord-Sud de la Péninsule Ibérique. La détection de 164 nouveaux haplotypes des lignées évolutives Africaines (lignée A) et Ouest-Méditerranéenne (lignée M) révèlent une diversité plus complexe que celle attendue avec la seule utilisation du test DraI. La distribution géographique des haplotypes décrits dans cette étude a permis d’une part, d’affiner le modèle évolutif de migration précédemment admis, décrivant une expansion du Sud-Ouest vers le Nord-Est et soutient d’autre part l’hypothèse d’une origine hybride des abeilles mellifères ibériques. La distribution géographique de chacune de ces lignées suggère la présence de deux refuges glaciaires situés au Nord-Est et au Sud de la Péninsule Ibérique. Cependant, la distribution géographique de l’haplotype AIII, confiné au Nord de la côte Atlantique de la Péninsule Ibérique tend à décrire un troisième refuge glaciaire, hypothèse qui mérite des recherches supplémentaires. Un arbre phylogénétique représentant 281 haplotypes, parmi lesquels 8 montrent des caractéristiques intermédiaires entre les lignées A et M, permet de classer l’ensemble des sous-lignées (AI, AII, AIII) et de la lignée M en groupes frères, et que par conséquent, ces haplotypes dériveraient probablement d’un ancêtre commun ayant les caractéristiques de l’actuelle sous-lignée Z. Ces découvertes suggèrent que la lignée évolutive M, aurait, non pas un ancêtre d’origine Nord-Africaine mais plutôt d’Afrique de l’Est et du Proche Orient, lieu où, est actuellement présente la sous-lignée Z. Le faible nombre de colonies (1 uniquement) portant un haplotype d’Europe de l’Est (lignée C) indique que les importations à but commercial sont résiduelles sur la péninsule Ibérique, contrastant avec d’autres régions de l’Europe de l’Ouest où les importations occasionnent un remplacement progressif de la sous-espèce native. Une analyse de sélection a été effectuée afin de déterminer si cette force évolutive a participé à la mise complexe de l’abeille Ibérique. Pour 1536 SNPs (GoldenGate Assay of Illumina) criblés sur les 711 faux-bourdons, seulement 383 se sont montrés être polymorphes. Tandis qu’un total de 69 SNPs on été identifiés utilisant deux méthodes de coalescence et deux méthodes Bayésiennes, seulement 17 sont validés par l’utilisation croisée des 4 méthodes. De plus, une méthode d’analyse spatiale a permis d’isoler 33 SNPs d’intérêt, parmi lesquels 28 coïncident avec les résultats précédents. Parmi les 17 SNPs, 10 témoignent d’un fort signal sélection (9 de type directionnelle et 1 de type balancée). 71 SNPs ont été situés au sein ou à proximité de gènes impliqués dans d’hypothétiques fonctions à rôle structural, de signalisation, métabolique, régulateur, de transport et d’immunité. Les mécanismes de vision, de détoxification xénobiotique et de réponses immunitaires sont clairement représentés par de nombreux gènes sous sélection. Pour le mécanisme de vision, cinq gènes sont responsables du développement neuronal, de la formation synaptique, du guidage axonal, de la régénération et de la production de chromophores (production de rhodopsine). Concernant la détoxification xénobiotique, trois gènes sont responsables de la tolérance aux toxines végétales et de la résistance aux insecticides. Enfin les 2 gènes en relation avec la réponse immunitaire innée participent aux mécanismes de phagocytose. L’analyse spatiale appuie le fait que la sélection est une force sous-jacente impliquée dans la mise en place de gradients latitudinaux et longitudinaux. La structure de la population à été obtenue à la fois grâce aux marqueurs maternel (région intergénique mitochondriale tRNAleu-cox2) et biparentaux (SNPs) sur la base de méthodes spatiales et non spatiales. La distribution géographique des lignées évolutives A e

Chloroplast genome of Tillandsia landbeckii Phil. (Bromeliaceae) a species adapted to the hyper-arid conditions of the Atacama and Peruvian desert

Tillandsia landbeckii Phil. is a vulnerable species belonging to the terrestrial Bromeliaceae family; it is highly adapted to extremely hyper-arid conditions of the Atacama Desert and Peruvian deserts. In this study, we sequenced, assembled, and annotated its chloroplast genome. T. landbeckii chloroplast genome is 159,131 bp in length, containing a large single-copy region of 87,164 bp, a small single-copy region of 18,521 bp, and a pair of inverted repeat regions of 26,723 bp. The GC content of the chloroplast genome is 37.33%. It encodes a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The phylogenetic tree indicates that T. landbeckii is placed within the Bromeliaceae family and has a close relationship with T. marconae with 100% support

Chloroplast genome of Tillandsia marconae till & Vitek (Bromeliaceae), a hyperarid desert endangered species

Tillandsia marconae Till & Vitek (Bromeliaceae) is a rare plant native species that grows over sand, in the coastal desert from Perú and Chile and is considered an endangered species. In this study, we assembled its chloroplast genome. The draft chloroplast genome of T. marconae is ca. 158,873 bp in length, containing a large single-copy region of 86,937 bp, a small single-copy region of 18,506 bp, and a pair of inverted repeat regions of 26,715 bp. The GC content of the draft chloroplast genome is 37.4%. It encodes a total of 135 genes, including 86 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and three pseudogenes. The phylogenetic tree indicated that T. marconae is placed within the Bromeliaceae family and a close relationship with Tillandsia usneoides with 100% support

Prediction of biometric variables through multispectral images obtained from UAV in beans (Phaseolus vulgaris L.) during ripening stage

Here, we report the prediction of vegetative stages variables of canary bean crop by means of RGB and multispectral images obtained from UAV during the ripening stage, correlating the vegetation indices with biometric variables measured manually in the field. Results indicated a highly significant correlation of plant height with eight RGB image vegetation indices for the canary bean crop, which were used for predictive models, obtaining a maximum correlation of R2 = 0.79. On the other hand, the estimated indices of multispectral images did not show significant correlations

Assessment of vegetation índices derived from UAV images for predicting biometric variables in bean during ripening stage

Here, we report the prediction of vegetative stages variables of canary bean crop employing RGB and multispectral images obtained from UAV during the ripening stage, correlating the vegetation indices with biometric variables measured manually in the field. Results indicated a highly significant correlation of plant height with eight vegetation indices derived from UAV images from the canary bean, which were evaluated by multiple regression models, obtaining a maximum correlation of R2 = 0.79. On the other hand, the estimated indices of multispectral images did not show significant correlations

Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper

In this study, we sequenced the first complete chloroplast (cp) genome of a Peruvian chili pepper landrace, “arnacucho” (Capsicum chinense). This cp genome has a 156,931 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (87,325 bp) and a 17,912 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (25,847 bp); and the percentage of GC content was 37.71%. Arnaucho chili pepper chloroplast genome possesses 133 genes that consists of 86 protein-coding genes, 37 tRNA, eight rRNA, and two pseudogenes. Phylogenetic analysis revealed that this Peruvian chili pepper landrace is closely related to the undomesticated species C. galapagoense; all belong to the Capsiceae tribe

Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper

In this study, we sequenced the first complete chloroplast (cp) genome of a Peruvian chili pepper landrace, “arnacucho” (Capsicum chinense). This cp genome has a 156,931 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (87,325 bp) and a 17,912 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (25,847 bp); and the percentage of GC content was 37.71%. Arnaucho chili pepper chloroplast genome possesses 133 genes that consists of 86 protein-coding genes, 37 tRNA, eight rRNA, and two pseudogenes. Phylogenetic analysis revealed that this Peruvian chili pepper landrace is closely related to the undomesticated species C. galapagoense; all belong to the Capsiceae tribe

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of de major lineages in the Rubiaceae family, and is an important timber tree, with origin in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct librar-ies. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and 01 pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotide (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than invert regions. Finally, phylogenetic analysis resolved that C. spruceanum is a sister species to Emmenopterys henryi, and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond

Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum), and Its Comparison with Other Solanaceae Species

Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native of the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes and tomatoes. To date, molecular tools for this crop are still undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum had a 155,681 bp in length with included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 88 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified, divided in mononucleotide repeats (32), followed by tetranucleotide (6) and dinucleotides (5). Microsatellites with trinucleotides repeats (3), pentanucleotide (1) and hexanucleotide (1) repeats motifs in these genomes were also identified, but in lower quantity. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect to provide useful molecular data to shed light on the genetic diversity within sweet cucumber landrace, and also to determine the evolutionary processes in S. muricatum