De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

Abstract

Quince (Cydonia oblonga Mill.) is the sole member of the genus Cydonia in the Rosacea family and closely related to the major pome fruits, apple (Malus domestica Borkh.) and pear (Pyrus communis L.). In the present work, whole genome shotgun paired-end sequencing was employed in order to assemble the first draft genome of quince. A genome assembly that spans 488.4 Mb of sequence corresponding to 71.2% of the estimated genome size (686 Mb) was produced in the study. Gene predictions via ab initio and homology-based sequence annotation strategies resulted in the identification of 25,428 and 30,684 unique putative protein coding genes, respectively. 97.4 and 95.6% of putative homologs of Arabidopsis and rice transcription factors were identified in the ab initio predicted genic sequences. Different machine learning algorithms were tested for classifying pre-miRNA (precursor microRNA) coding sequences, identifying Support Vector Machine (SVM) as the best performing classifier. SVM classification predicted 600 putative pre-miRNA coding loci. Repetitive DNA content of the assembly was also characterized. The first draft assembly of the quince genome produced in this work would constitute a foundation for functional genomic research in quince toward dissecting the genetic basis of important traits and performing genomics-assisted breeding.

Taihangia rupestris: First Genome Survey and Microsatellite Motif Identification

“…Here, after adjusting for the K-mer, the corrected genome size of T. rupestris was 976.97 Mb. These estimates were greater than those of F. vesca (240 Mb) [22], Pyrus bretschneideri (527 Mb) [23], Ficus erecta (341 Mb) [24], and C. oblonga (686 Mb) [18]; smaller than those of Arachis duranensis (1.25 Gb) [25], Lupinus angustifolius (1.15 Gb) [26], and Prunus fruticose (1.2 Gb) [27]; and similar to those of Begonia fuchsioides (935 Mb) [28] and Quercus suber (953 Mb) [29]. Based on the heterozygosity and repetition, the genome was divided into low-heterozygosity (≥50%), micro-heterozygosity (0.5%-0.8%), high-heterozygosity (≥0.8%), and high-repetition (repeated ratio ≥50%), which directly reflects the difficulty of assembling the subsequent sequencing data [12,30].…”

“…The density points were mostly found in the 20% to 50% GC content level, with the average being 33.75%. It is similar to those of Apocynum venetum (32.91%) [16] and Macaranga indica (33.83%) [17], but lower than those of Cydonia oblonga (38.66%) [18], Rosa multiflora (38.9%) [19], Fragaria nilgerrensis (39.22%) [20], and Rosa rugosa (39.30%) [21]. Thus, the genome of T. rupestris has a mid-level GC content.…”

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

“…The proportion of repetitive elements in the cashew genome is smaller compared to the 70% in Pistacia vera , a member of Anacardiaceae family, draft genome suggesting that repetitive elements increase with an increase in genome sizes 55 . However, greater proportions of long terminal repeats (LTRs) and unclassified elements which are similar to that are found in the P. vera 55 and other plants 63 . In general, the mobility of transposons and retroelements contributes to the expansion and evolution of plant genomes and may alter gene expressions by epigenetic modifications 64 , 65 .…”

Identification of self-incompatibility alleles in Quince (Cydonia oblonga Mill.)

“…Quince ( Cydonia oblonga Mill., 2n = 2x = 34), a member of the Rosaceae family, is predominantly found in temperate regions globally, tracing its origins to Western Asia, notably in the northern regions of Iran, Turkmenistan, the Caucasus, Armenia, Azerbaijan, and the Russian Federation [ 1 , 2 ]. Ranking as the third most economically significant fruit tree in the pome fruit subgroup, following apples and pears [ 3 ], quince is celebrated for its health-enhancing attributes, attributed to its robust antioxidant activities and rich phenolic content [ 4 ].…”