The chloroplast protein HCF164 is predicted to be associated with Coffea SH 9 resistance factor against Hemileia vastatrix

This work was funded by Portuguese national funds through FCT—Fundação para a Ciência e Tecnologia, I.P., under the Projects: UID/AGR/04129/2020 of LEAF; UIDP/04378/2020 and UIDB/04378/2020 of UCIBIO; and LA/P/0140/2020 of i4HB and FCT and FEDER funds through PORNorte under the projects: HDT-Coffee (PTDC/ASP-PLA/32429/2017) and CoffeeRES (PTDC/ASP-PLA/29779/2017). H.A. was supported by Portuguese national funds through FCT within the scope of the Stimulus of Scientific Employment—Individual Support (CEECIND/00399/2017/CP1423/CT0004). A.O. was supported at the University of Bristol by Oracle for Research and the Biological and Biotechnological Sciences Research Council ([BB/X009831/1] and [BBW003449/1]). All molecular modelling work was carried out using the computational facilities of the Advanced Computing Research Centre, University of Bristol (http://www.bris.ac.uk/acrc).To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid “Híbrido de Timor”. Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.CoffeeRES CEECIND/00399/2017/CP1423/CT0004, PTDC/ASP-PLA/29779/2017University of Bristol by Oracle for ResearchBiotechnology and Biological Sciences Research Council BB/X009831/1, BBW003449/1 BBSRCUniversity of BristolFundação para a Ciência e a Tecnologia LA/P/0140/2020, UID/AGR/04129/2020, UIDB/04378/2020, UIDP/04378/2020 FCTEuropean Regional Development Fund PTDC/ASP-PLA/32429/2017 ERD

Body size variation in a lineage of spur-thighed tortoises (Testudo graeca whitei) contrasts with that expected from the species level

Ectotherms exhibit varying geographic size patterns shaped by environmental and evolutionary factors. This variability is noticeable within taxonomic groups. For instance, certain testudinids follow Bergmann’s rule (body size increases with latitude) and Rensch’s rule (sexual size dimorphism correlates with body size), while others do not. Here we hypothesize that body size patterns can even vary within a monophyletic lineage. To address this, we evaluated the body size patterns of the spur-thighed tortoise Testudo graeca that globally follows Bergmann’s and Rensch’s rules. We specifically investigated the influence of climate variables, latitude and elevation within the subspecies T. g. whitei throughout its natural distribution in North Africa, and in a recently expanded range in SE Spain (20 kya old). We found that males were smaller than females in both regions. The tortoises from SE Spain were smaller than those from North Africa, which showcased the smallest sizes ever reported for the species. Latitude was the main variable to explain tortoise body size. In particular, body size decreased with latitude in both regions, which contrasts with Bergmann’s rule expectations based on species-level findings. Finally, to further contradict species-level expectations, we did not find any statistical correlation between sexual size dimorphism and body size across the two studied regions. Such contradictory outcomes reveal complex geographic size patterns within T. graeca and raise conservation questions about demographic viability at smaller-sized sites.This work was supported by Projects PID2019-105682RA-I00 and TED2021-130381B-I00, funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033), the last also with the support of the European Union “NextGenerationEU”/PRTR”; and by funding from the Regional Valen cian Government (AICO/2021/145). The Miguel Hernández University provided support for several stays of MJS in the Ecology Area of the university. RCRC is supported by the European Union-Next Generation EU in the Maria Zambrano Programme (ZAMBRANO 21-26). The Dirección General de Gestión del Medio Natural of Andalusian Government (SGB/FOA/AFR), the Dirección General de Medio Natural of the Murcia Region and the Ministère de l’Agriculture, de la Pêche Maritime, du Développement Rural et des Eaux et Forêts Pêche Maritime, Département des Eaux et Forêts, decisión No. 19/2022 (DEF/DLCDPN/DPRN/CFF), authorized and facilitated sampling

Shorter telomeres are associated with shell anomalies in a long-lived tortoise

Age-related telomere length (TL) variation is relatively well-described for mammals, birds and other model organisms. Nevertheless, it remains largely unknown in ectotherms, especially turtles and tortoises, which are extremely long-lived species with slow or negligible senescence. In this study, we described TL dynamics in wild spur-thighed tortoises (Testudo graeca), one of the chelonian species with the lowest aging rates. By combining cross-sectional (single) and longitudinal (capture–recapture) samplings, we assessed the relationship between TL and individual characteristics (sex, age, individual growth rate, body condition index, presence of shell anomalies). We did not find any association between TL and sex, individual growth rate, or body condition. However, the relationship with age remains uncertain, likely due to the complex dynamics of TL over time. Interestingly, shorter telomeres correlated significantly with shell anomalies, which are usually assumed as a fitness proxy for reptiles. Overall, our results suggest TL as a potential indicator for ontogenetic studies on tortoises, while its utility as a marker of biological age appears limited.This work was supported by Project PID2019-105682RA-I00 and TED2021-130381B-I00, funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033), the last also with the support of the European Union ‘NextGenerationEU/PRTR’. RCRC is supported by the European Union-Next Generation EU in the Maria Zambrano Programme (ZAMBRANO 21-26)

Potential association of HCF164, a chloroplast nuclear-encoded thioredoxin-like protein, with Coffea SH9 resistance factor against Hemileia vastatrix

29th Conference of Association for the Science and Information on Coffee, 11 Sept. - 14 Sept. 2023 Hanoi, Vietnaminfo:eu-repo/semantics/publishedVersio

Body size variation in a lineage of spur-thighed tortoises (<i>Testudo graeca whitei</i>) contrasts with that expected from the species level

Ectotherms exhibit varying geographic size patterns shaped by environmental and evolutionary factors. This variability is noticeable within taxonomic groups. For instance, certain testudinids follow Bergmann's rule (body size increases with latitude) and Rensch's rule (sexual size dimorphism correlates with body size), while others do not. Here we hypothesize that body size patterns can even vary within a monophyletic lineage. To address this, we evaluated the body size patterns of the spur-thighed tortoise Testudo graeca that globally follows Bergmann’s and Rensch’s rules. We specifically investigated the influence of climate variables, latitude and elevation within the subspecies T. g. whitei throughout its natural distribution in North Africa, and in a recently expanded range in SE Spain (20 kya old). We found that males were smaller than females in both regions. The tortoises from SE Spain were smaller than those from North Africa, which showcased the smallest sizes ever reported for the species. Latitude was the main variable to explain tortoise body size. In particular, body size decreased with latitude in both regions, which contrasts with Bergmann’s rule expectations based on species-level findings. Finally, to further contradict species-level expectations, we did not find any statistical correlation between sexual size dimorphism and body size across the two studied regions. Such contradictory outcomes reveal complex geographic size patterns within T. graeca and raise conservation questions about demographic viability at smaller-sized sites.</p

The chloroplast protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix

Abstract To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid “Híbrido de Timor”. Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs

Publisher Correction: The chloroplast protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix

Publisher Copyright: © 2023, Springer Nature Limited.Correction to: Scientific Reports, published online 25 September 2023 The original version of this Article contained an error in Figure 3, panels B and C, where the results were incorrectly displayed. (Figure presented.) Analysis of the HCF164 sequence in chromosome 7c (C. canephora-derived sug-genome): (A) Depiction of the variants identified in the genomic region encoding the HCF164 protein in chromosome 7c following the reference genome annotation (GCA_003713225). The diagram shows the ORF (composed of five exons represented as grey rectangles) and 2 kbp upstream and downstream flanking regions. The numbers in brackets represent the number of variants identified in the 25 studied individuals, whereas the numbers in bold represent variants potentially associated with the SH9 factor (that is, variants exclusively found in SH9 individuals). (B) Haplotype network of the genomic region encoding the HCF164 protein (including 2 kbp flanking regions) obtained for the 25 studied individuals. (C) Schematic view of the alignment of the three HCF164 protein isoforms predicted in the 25 studied individuals. The thioredoxin domain and the redox-active disulphide center are highlighted in white and black, respectively. Orange represents SH9 individuals and blue represents non-SH9 individuals. The original Article has been corrected.publishersversionepub_ahead_of_prin