Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing
<i>Capsicum annuum</i> var. <i>glabriusculum</i> is an economically important horticultural crop and is considered the wild genetic ancestor of chili peppers. The distribution range extends from southern North America, through Central America, to South America. Approximately...
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2024-11-01
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| author | Valeria Itzel Moreno-Contreras Ma. Carmen E. Delgado-Gardea Jesús A. Ramos-Hernández Alfonso Mendez-Tenorio Hugo Varela-Rodríguez Blanca Sánchez-Ramírez Zilia Y. Muñoz-Ramírez Rocío Infante-Ramírez |
| author_facet | Valeria Itzel Moreno-Contreras Ma. Carmen E. Delgado-Gardea Jesús A. Ramos-Hernández Alfonso Mendez-Tenorio Hugo Varela-Rodríguez Blanca Sánchez-Ramírez Zilia Y. Muñoz-Ramírez Rocío Infante-Ramírez |
| author_sort | Valeria Itzel Moreno-Contreras |
| collection | DOAJ |
| description | <i>Capsicum annuum</i> var. <i>glabriusculum</i> is an economically important horticultural crop and is considered the wild genetic ancestor of chili peppers. The distribution range extends from southern North America, through Central America, to South America. Approximately 226 million 150 paired-end reads were generated from CHMX_Ch1 (a <i>C. annuum</i> from Chihuahua, Mexico). To compare with the CHMX_Ch1 genome, high-quality reads from QO (a <i>C. annuum</i> from Querétaro, Mexico) were downloaded from the NCBI database. A total of 210,324 variants were detected in CHMX_Ch1, whereas 169,718 variants were identified in QO, all compared to the domesticated <i>C. annuum</i> reference genome, UCD10Xv1.1. This comprised 203,990 SNPs and 6334 InDels in CHMX_Ch1 and 164,955 SNPs and 4763 InDels in QO. The variants with high and moderate impact were identified as missense, splice acceptor, splice donor, start lost, stop gain, stop lost, frameshift, insertion, and deletion effects. The candidate genes with the highest fold enrichment values among the SNPs were predominantly involved in gene regulation and metabolic processes. InDels were associated with nuclear and transcriptional regulator activity in both genomes. Overall, a greater number of variants were found in CHMX_Ch1 compared to QO. This study provides knowledge of the principal functions associated with high- and moderate-impact variants and supplies a resource for further investigations of the genetic characteristics of these chiltepin peppers. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-11-01 |
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| spelling | doaj-art-2db250c8fef043cbbd1348468f9f867c2024-11-26T18:19:06ZengMDPI AGPlants2223-77472024-11-011322324810.3390/plants13223248Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome SequencingValeria Itzel Moreno-Contreras0Ma. Carmen E. Delgado-Gardea1Jesús A. Ramos-Hernández2Alfonso Mendez-Tenorio3Hugo Varela-Rodríguez4Blanca Sánchez-Ramírez5Zilia Y. Muñoz-Ramírez6Rocío Infante-Ramírez7Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoFacultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoFacultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoLaboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, MexicoFacultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoFacultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoFacultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, MexicoFacultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua 31125, Mexico<i>Capsicum annuum</i> var. <i>glabriusculum</i> is an economically important horticultural crop and is considered the wild genetic ancestor of chili peppers. The distribution range extends from southern North America, through Central America, to South America. Approximately 226 million 150 paired-end reads were generated from CHMX_Ch1 (a <i>C. annuum</i> from Chihuahua, Mexico). To compare with the CHMX_Ch1 genome, high-quality reads from QO (a <i>C. annuum</i> from Querétaro, Mexico) were downloaded from the NCBI database. A total of 210,324 variants were detected in CHMX_Ch1, whereas 169,718 variants were identified in QO, all compared to the domesticated <i>C. annuum</i> reference genome, UCD10Xv1.1. This comprised 203,990 SNPs and 6334 InDels in CHMX_Ch1 and 164,955 SNPs and 4763 InDels in QO. The variants with high and moderate impact were identified as missense, splice acceptor, splice donor, start lost, stop gain, stop lost, frameshift, insertion, and deletion effects. The candidate genes with the highest fold enrichment values among the SNPs were predominantly involved in gene regulation and metabolic processes. InDels were associated with nuclear and transcriptional regulator activity in both genomes. Overall, a greater number of variants were found in CHMX_Ch1 compared to QO. This study provides knowledge of the principal functions associated with high- and moderate-impact variants and supplies a resource for further investigations of the genetic characteristics of these chiltepin peppers.https://www.mdpi.com/2223-7747/13/22/3248bioinformaticschili peppervariant callingwhole genome sequencingmolecular markers |
| spellingShingle | Valeria Itzel Moreno-Contreras Ma. Carmen E. Delgado-Gardea Jesús A. Ramos-Hernández Alfonso Mendez-Tenorio Hugo Varela-Rodríguez Blanca Sánchez-Ramírez Zilia Y. Muñoz-Ramírez Rocío Infante-Ramírez Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing Plants bioinformatics chili pepper variant calling whole genome sequencing molecular markers |
| title | Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing |
| title_full | Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing |
| title_fullStr | Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing |
| title_full_unstemmed | Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing |
| title_short | Genome-Wide Identification and Characterization of SNPs and InDels of <i>Capsicum annuum</i> var. <i>glabriusculum</i> from Mexico Based on Whole Genome Sequencing |
| title_sort | genome wide identification and characterization of snps and indels of i capsicum annuum i var i glabriusculum i from mexico based on whole genome sequencing |
| topic | bioinformatics chili pepper variant calling whole genome sequencing molecular markers |
| url | https://www.mdpi.com/2223-7747/13/22/3248 |
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