Abstract
Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.
Highlights
The cp genomes of most gymnosperms are uniparentally paternally inherited, whereas the majority of angiosperms are uniparentally maternally inherited [1]
At least 5.74 GB of clean data was obtained for Q. bawanglingensis, and these data were assembled into a double-stranded circular DNA with a length of 161,394 bp (Figure 1 and Table 1)
The maximum difference in genome size among the nine Fagaceae species is 3055 whereas the largest difference in the large single-copy (LSC) region is 2981 bp, which could indicate that the divergence in bp, whereas the largest difference in the LSC region is 2981 bp, which could indicate that the the LSC length leads to variation in the size of the cp genomes based on inverted repeats (IRs) contraction or expansion [31]
Summary
The cp genomes of most gymnosperms are uniparentally paternally inherited, whereas the majority of angiosperms are uniparentally maternally inherited [1]. The cp genomes, which encode approximately 130 genes and range from 76 to 217 kb [2,3], are typical double-stranded circular DNA composed of four regions containing two copies of inverted repeats (IRa and IRb) and two Forests 2019, 10, 0587; doi:10.3390/f10070587 www.mdpi.com/journal/forests. The availability of sufficient data on cp genomes is crucial for phylogenetic relationship reconstruction, i.e., the assessment of relationships within angiosperms [10,11,12], the identification of members of Pinaceae [13] and Pinus [14], and adequate comparisons, i.e., cp genomes from sister species [15] and possibly multiple individuals [16]. Approximately 3000 plastid genomes of Eukaryota are shareable in the National Center for Biotechnology Information database Molecular genetic methodologies based on nuclear and organellar genomes are crucial for conservation studies [17], the conservation of threatened species for which there is scarce information on the genetic variation among populations [18]
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