Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding. 

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De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination

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Mitochondria, inherited maternally, are energy metabolism organelles that generate most of the chemical energy needed to power cellular various biochemical reactions. Deciphering mitochondrial genome (mitogenome) is important for elucidating vital activities of species. The complete chloroplast (cp) and nuclear genome sequences of Populus simonii (P. simonii) have been reported, but there has been little progress in its mitogenome. Here, we assemble the complete P. simonii mitogenome into three circular-mapping molecules (lengths 312.5, 283, and 186 kb) with the total length of 781.5 kb. All three molecules of the P. simonii mitogenome had protein-coding capability. Whole-genome alignment analyses of four Populus species revealed the fission of poplar mitogenome in P. simonii. Comparative repeat analyses of four Populus mitogenomes showed that there were no repeats longer than 350 bp in Populus mitogenomes, contributing to the stability of genome sizes and gene contents in the genus Populus. As the first reported multi-circular mitogenome in Populus, this study of P. simonii mitogenome are imperative for better elucidating their biological functions, replication and recombination mechanisms, and their unique evolutionary trajectories in Populus.

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Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Sapindus mukorossi (S. mukorossi) is an important biological washing material and biomass energy tree species whose peel is rich in saponins, and its kernels have a high oil content. We used the maximum entropy model (MaxEnt) to predict the suitable habitats of S. mukorossi globally, screen the dominant environmental factors affecting its distribution and analyse the changes in its suitable habitats under climate change from prehistory to the future, and the results will provide a scientific basis for germplasm resource collection, protection, introduction and cultivation. Twenty-two environmental variables and global distribution data for S. mukorossi were used to construct the species distribution model, and the receiver operating characteristic (ROC) curve was used to verify the accuracy of the model. The dominant environmental factors were screened through the jackknife method, and then, the geographical information system (ArcGIS) was used to complete the grade of suitable habitat division and area calculation. The results showed that the MaxEnt model had an excellent predictive effect, and the area under the ROC curve (AUC) value was as high as 0.969. The precipitation of the warmest quarter (Bio18), the minimum temperature of the coldest month (Bio6), temperature seasonality (Bio4) and isothermality (Bio3) were the dominant environmental factors that affected the distribution of S. mukorossi. The largest area of the world’s suitable habitats occurred during the last interglacial (LIG) (772.69 × 104 km2), and the area decreased sharply (614.46 × 104 km2) during the last glacial maximum (LGM). The area of suitable habitat showed an increasing trend during the Mid-Holocene (MH) and currently, with areas of 631.06 × 104 km2 and 706.82 × 104 km2, respectively. The area of suitable habitats for S. mukorossi globally was 718.35 × 104 km2 (SSP1-2.6), 636.85 × 104 km2 (SSP2-4.5), 657.64 × 104 km2 (SSP3-7.0) and 675.89 × 104 km2 (SSP5-8.5) under the four scenarios of the future climate. The area increased only in the SSP1 scenario. In summary, globally, the suitable area of S. mukorossi tended to migrate to higher latitudes and decrease in area with future climate change.

Predicting the potential global distribution of Sapindus mukorossi under climate change based on MaxEnt modelling

In the present study, we depicted the complete mitochondrial genome of a valuable medicinal plant, Vitex rotundifolia. The mitochondrial genome of V. rotundifolia, mapped as a circular molecule, spanned 380,980 bp in length and had a GC content of 45.54%. The complete genome contained 38 protein-coding genes, 19 transfer RNAs (tRNAs), and 3 ribosomal RNAs (rRNAs). We found that there were only 38.73% (147.54 kb), 36.28% (138.23 kb), and 52.22% (198.96 kb) of the homologous sequences in the mitochondrial genome of V. rotundifolia, as compared with the mitochondrial genomes of Scutellaria tsinyunensis, Boea hygrometrica, and Erythranthe lutea, respectively. A multipartite structure mediated by the homologous recombinations of the three direct repeats was found in the V. rotundifolia mitochondrial genome. The phylogenetic tree was built based on 10 species of Lamiales, using the maximum likelihood method. Moreover, this phylogenetic analysis is the first to present the evolutionary relationship of V. rotundifolia with the other species in Lamiales, based on the complete mitochondrial genome.

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Sequence Analysis of the Complete Mitochondrial Genome of a Medicinal Plant, Vitex rotundifolia Linnaeus f. (Lamiales: Lamiaceae)

Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China


 Background: Sapindus is an important biodiesel, biomedical, and multifunctional economic forest species in Asia, however its germplasms have been persistently damaged or lost. It is imperative to conserve the diversity of Sapindus. This study aimed to reveal the potential habitat distribution patterns of Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in response to current environment and future climate change, and identify hotspots of habitat degradation/expansion to facilitate climate change-adaptive biological conservation. Methods: Using current environmental data and future climate projections (2021–2100), we simulated the present and potential future habitats of Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in east and southeast Asia using a maximum entropy (MaxEnt) model that was developed based on 2041 occurrence records. Results: The model showed that precipitation may play an important role in framing the potential habitats of Sapindus; however, S. delavayi was more sensitive to minimum temperatures (-2 °C to 3 °C) and elevation (1200-2000 m), while S. rarak was more demanding in terms of solar radiation (annual mean Uvb of 4600 to 5000 J/m2/day). Under the current environment, S. mukorossi has the widest suitable habitat distribution (250.24 × 104 km2), followed by that of S. rarak (173.49 × 104 km2), and S. delavayi (78.85 × 104 km2). Under future climate change scenarios, the habitat distribution of S. mukorossi will expand and contract, that of S. delavayi exhibited significant expansion. In contrast, future S. rarak habitat distribution exhibited significant contraction. Conclusions: There were significantly distinct ecological adaptations among Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in east and southeast Asia. The contraction areas should be subject to germplasm collection and ex situ conservation preferentially. The modelled unchanged areas should be used for potential future Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak conservation and utilization.

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Shuanglong Shi

Papers

Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China

Distinct Ecological Adaptations and Habitat Responses to Future Climate Change in Three East and Southeast Asian Sapindus Species