Next-generation sequencing yields the complete chloroplast genome of Abies kawakamii

Development of a highly polymorphic chloroplast SSR set in Abies grandis with transferability to other conifer species-A promising toolkit for gene flow investigations

The genus Abies is widely distributed across the world and is of high importance for forestry. Since chloroplasts are usually uniparentally inherited, they are an important tool for specific scientific issues like gene flow, parentage, migration and, in general, evolutionary analysis. Established genetic markers for organelles in conifers are rather limited to RFLP markers, which are more labour and time intensive, compared with SSR markers. Using QUIAGEN CLC Workbench 23.03, we aligned two chloroplast genomes from different Abies species (NCBI accessions: NC_039581, NC_042778, NC_039582, NC_042410, NC_035067, NC_062889, NC_042775, NC_057314, NC_041464, MH706706, MH047653 and MH510244) to identify potential SSR candidates. Further selection and development of forward and reverse primers was performed using the NCBI Primer Blast Server application. In this article, we introduce a remarkably polymorphic SSR marker set for various Abies species, which can be useful for other conifer genera, such as Cedrus, Pinus, Pseudotsuga or Picea. In total, 17 cpSSRs showed reliable amplification and polymorphisms in A. grandis with a total of 68 haplotypes detected. All 17 cpSSRs amplified in the tested Abies spp. In the other tested species, except for Taxus baccata, at least one primer was polymorphic.

The complete chloroplast genome of Keteleeria evelyniana Mast var. pendula Hsüeh (Pinaceae), a species with extremely small populations in China

Keteleeria evelyniana Mast var. pendula Hsüeh, a typical plant species of extremely small population, is faced to be endangered. The complete chloroplast (cp) genome of K. evelyniana var. pendula has been assembled and annotated for the first time in this study. The complete genome in length was found to be 117,139 bp. The genome annotation revealed a total of 118 genes, including 34 transfer RNA (tRNA) genes, 4 ribosomal RNA (rRNA) genes, and 80 protein-coding genes. The maximum-likelihood phylogenetic tree supported that K. evelyniana var. pendula, K. fortune, K. evelyniana, and K. davidiana are clustered in one branch. This complete chloroplast genome helped us to understand the evolution of K. evelyniana var. pendula. These results laid the foundation for future studies on the conservation of this species.

Complete chloroplast genome features and phylogenetic analysis of Abies ernestii var. salouenensis (Bordères and Gaussen) W. C. Cheng and L. K. Fu from southwest China

Abies ernestii var. salouenensis (Bordères & Gaussen) W. C. Cheng & L. K. Fu is endemic to southwest China, including the southeastern Tibetan Plateau and the northwestern Yunnan Province. The taxonomic relationships between A. ernestii var. salouenensis and two other closely related fir species (A. chensiensis Tiegh. and A. ernestii Rehd.) still need to be determined. Here, we report for the first time the whole chloroplast genome of A. ernestii var. salouenensis. Its genome is 121,759 bp long and is characterized by a circular structure with 68 peptide-encoding genes, 16 tRNAs, six ORFs, and four rRNAs. We also identified 70 microsatellite repeat sequences and 14 tandem repeat sequences in the chloroplast genome of A. ernestii var. salouenensis. Comparative genome analysis indicated considerable variation in ycf1 and ycf2. Phylogenetic analysis supported the monophyly of A. ernestii var. salouenensis, A. chensiensis Tiegh., and A. ernestii Rehd. The relationships among them should be surveyed using more samples at the species level. This study will facilitate taxonomic studies and the development of suitable chloroplast markers for fir species.

The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation

BACKGROUND

Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied.

RESULTS

Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs.

CONCLUSIONS

The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.

The complete chloroplast genome of Abies ernestii Rehder (Pinaceae) and its phylogenetic implications

Abies ernestii Rehder is endemic to the montane regions of Southwest China. Till now, phylogenetic relationships between A. ernestii and other closely related species remain unclear. In this study, we first characterized the complete chloroplast (cp) genome of A. ernestii. The whole cp genome was 121,841 bp in size, including one hundred and thirteen genes. Results of comparative cp genome revealed that only ycf1 and ycf2 was characterized by a considerable variation. Our phylogenetic analyses supported the monophyly of the genus Abies and revealed a clear separation between A. ernestii and A. chensiensis Tiegh. This study highlights the significance of using cp genomes to examine species boundaries among closely related fir species.

Characterization of the complete plastid genome of Abies forrestii (Pinaceae) from southwest China

Abies forrestii is endemic to southwest China and ecologically important as a major component of the cold temperate forests. This study was the first report complete chloroplast (cp) genome of A. forrestii. The complete chloroplast genome was 120,022 bp in size. In total, 114 genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Thirteen genes contain introns. In phylogenetic analysis, A. forrestii was found to be closely related with A. nukiangensis, A. fanjingshanensis and A. delavayi subsp. fansipanensis. Our study will provide potential genetic resources for further evolutionary studies of this ecologically important species.