Figure 3 - available via license: Creative Commons Attribution 4.0 International
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The circular chloroplast genome map of Carya (take C. cordiformis as reference graph). The genes shown inside and outside of the circle are transcribed in clockwise and counterclockwise directions, respectively. Genes from different functional groups are shown in different colors. The thick dark lines in inner circle show the extent of the Inverted repeats (IRA and IRB) separating the Large Single-Copy (LSC) and the Small Single-Copy (SSC) regions. The gray ring represents the GC content. The circular chloroplast genome maps of 10 species were show in Figure S1.
Source publication
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of...
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Context 1
... first obtained the raw sequencing data of 10 species of the Carya genus (Table S1). Then, we assembled the 10 complete closed-loop chloroplast genomes of these species ( Figure 3 and Figure S1) for the analysis below. From the assemblies, we learned that the average size of the 10 species was about 160 kb ( Table 1). ...
Citations
... The topologies inferred from the chloroplast genomes are shown in Fig. 2 (left). Carya was reconstructed as monophyletic with a strong support value (MP-BS = 100%, ML-BS = 100%, PP-BI = 1.00), which is consistent with previous studies (Zhang et al. 2013, Luo et al. 2021). The phylogenetic relationships indicate that the newly identified species is a sister to Carya tonkinensis with high support values (MP-BS = 100%, ML-BS = 100%, PP-BI = 1.00). ...
Carya luana sp. nov., a new species of Juglandaceae from Guizhou, China, is described and illustrated. The new species is easily distinguished from other Carya species by having lanceolate leaflets and obovate fruits with a 4–6 mm thick husk, but is otherwise morphologically close to C. tonkinensis and C. kweichowensis . Based on phylogenetic reconstruction of whole plastomes, C. luana is the sister of C. tonkinensis , while formed a clade with C. tonkinensis and C. hunanensis on ITS. A morphometric analysis demonstrate that C. luana , C. tonkinensis and C. kweichowensis are morphologically distinct. The conservation status of C. luana is assessed as Endangered (EN) according to the IUCN Red List Categories and Criteria. A new identification key to all Asian Carya species is provided.
... In the original publication [1], there was a mistake in Table 2 as published. Minor errors were found in the number of tRNA and rRNA genes, CDS length and GC content in Table 2. ...
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
