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The complete chloroplast genome and phylogenetic analysis of Citrus clementina (Rutaceae).

ABSTRACT: Citrus, which is widely cultivated in tropical and subtropical climates, is one of the most important crops in the world. Here, we assembled and annotated the complete chloroplast genome of Citrus clementina (C. clementina) using Illumina sequencing data. This chloroplast genome exhibited a typical quadripartite structure of 154,042 bp in length, and the overall GC content was 38.42%. A total of 134 genes (90 protein-coding genes, 36 tRNAs, and eight rRNAs) were predicted in this chloroplast genome. Phylogenetic analysis strongly supported that C. clementina was evolutionarily close to Citrus sunki.

SUBMITTER: Sun C

PROVIDER: S-EPMC8439215 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundWith the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species.ResultsFifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.ConclusionsA set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata.

Dataset Information

The complete chloroplast genome and phylogenetic analysis of Citrus clementina (Rutaceae).

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