Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae

Abstract

Eriobotrya japonica (Thunb.) Lindl (loquat) is an evergreen Rosaceae fruit tree widely distributed in subtropical regions. Its leaves are considered as traditional Chinese medicine and are of high medical value especially for cough and emesis. Thus, we sequenced the complete plastid genome of E. japonica to better utilize this important species. The complete plastid genome of E. japonica is 159,137 bp in length, which contains a typical quadripartite structure with a pair of inverted repeats (IR, 26,326 bp) separated by large (LSC, 89,202 bp) and small (SSC, 19,283 bp) single-copy regions. The E. japonica plastid genome encodes 112 unique genes which consist of 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene structure and content of E. japonica plastid genome are quite conserved and show similarity among Rosaceous species. Five large indels are unique to E. japonica in comparison with Pyrus pyrifolia and Prunus persica, which could be utilized as molecular markers. A total of 72 simple sequence repeats (SSRs) were detected and most of them are mononucleotide repeats composed of A or T, indicating a strong A or T bias for base composition. The Ka and Ks ratios of most genes are lower than 1, which suggests that most genes are under purifying selection. The phylogenetic analysis described the evolutionary relationship within Rosaceae and fully supported a close relationship between E. japonica and P. pyrifolia. Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3702-3) contains supplementary material, which is available to authorized users.

The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

“…The highest divergence in non-coding regions was found for rps16 - trnQ , petN - psbM , ndhC - trnV , petA - psbL and rpl32 - ccsA . These results are similar to those of other analyses performed in Rosaceae ( Wang, Shi & Gao, 2013 ; Shen et al, 2016 ), suggesting that these regions evolve rapidly in Rosaceae.…”

“…Two genes with internal stop codons ( ycf15 and ycf68 ) and one without a stop codon ( infA ) were annotated as pseudogenes. Absence or pseudogenization of these three genes has also been reported in other Rosaceae species, such as Eriobotrya japonica ( Shen et al, 2016 ) and Prinsepia utilis ( Wang, Shi & Gao, 2013 ). The rps12 gene is a trans-spliced gene with a 5′ exon located in an LSC region and two 3′ exons located in IR regions.…”

“…The GC content of the chloroplast genome is 37.23% ( Table 1 ), and the GC contents of the LSC and SSC regions (35.12% and 31.14%) are lower than those of the IR regions (42.85%). The high GC contents in the IR regions are mainly due to the high GC contents of the four ribosomal RNA (rRNA) genes (55.43%) which is similar to most of other plants cp genomes ( Wang, Shi & Gao, 2013 ; Shen et al, 2016 ; Kong & Yang, 2017 ).…”

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species

“…The introns of rpl2, rps16, ndhA, trnV, clpP , and ndhA were relatively highly divergent, too. These results might indicate that these regions evolve rapidly in the genus Rosa , as well as in other Rosaceae plants [ 26 , 27 ].…”

Complete plastome of a subtropical tree Eriobotrya malipoensis (Rosaceae) in Yunnan

“…104.852021 E, Lat. 23.146254N, 1292 m), using the modified CTAB method (Shen et al 2016). The voucher specimen was preserved in the Herbarium of Southwest Forestry University (Accession Number: SWFU-SY35055).…”