bims-plasge 2018-09-16 papers

Mol Phylogenet Evol. 2018 Sep 06. pii: S1055-7903(18)30283-5. [Epub ahead of print]

Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes.

Vera S Bogdanova, Anatoliy V Mglinets, Natalia V Shatskaya, Oleg E Kosterin, Vladimir I Solovyev, Gennadiy V Vasiliev.

Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions. The positions of three accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, two accessions, from the Black Sea area of Turkey and Georgia, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. We suppose these unusual plastid genomes to be ancient lineages ascending to a 'missing link' between P.fulvum and P.sativum, represented by accession Pe 013 from Turkey. Accessions with common pea appearance but deeply diverged plastids could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas.

Keywords: Pisum L.; introgression; phylogenetic trees; plant microevolution; plastid genome; wild peas

DOI: https://doi.org/10.1016/j.ympev.2018.09.002

Mol Phylogenet Evol. 2018 Sep 06. pii: S1055-7903(18)30214-8. [Epub ahead of print]

Phylogenomics, biogeography, and adaptive radiation of grapes.

Zhi-Yao Ma, Jun Wen, Stefanie M Ickert-Bond, Ze-Long Nie, Long-Qing Chen, Xiu-Qun Liu.

The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources. In this study, we obtained whole-genome sequence data from 41 accessions representing most taxa within subgenus Vitis and aligned these sequences to the Vitis vinifera L. reference genome. We reconstructed deep phylogenetic relationships within subgenus Vitis based on 2,068 single-copy orthologous genes, which led to a robust topology with bootstrap support values of 100% for almost all branches. Three main clades are recovered within subgenus Vitis reflecting their continental distribution through North America, Europe, and East Asia, respectively. Our results suggest that the most possible migration route of the East Asian Vitis is from northeastern Asia southward to South Asia and Southeast Asia. The East Asian Vitis seems to have experienced adaptive radiation during the Miocene. This study provides novel insights into the diversification history of the grape genus Vitis.

Keywords: Vitis; adaptive radiation; evolutionary diversification; genome resequencing; phylogenetics

DOI: https://doi.org/10.1016/j.ympev.2018.08.021

Mol Phylogenet Evol. 2018 Sep 05. pii: S1055-7903(17)30337-8. [Epub ahead of print]

Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum.

Aaron Floden, E E Schilling.

Polygonatum is a widespread temperate genus with approximately 75 species centered in the Eastern Himalaya and Indo-Burma biodiversity hotspots. A complete assessment of the remarkable diversity of Polygonatum in these areas requires an accurate circumscription of the genus, as well as a clear understanding of generic and infrageneric relationships, both of which have been problematic in the past. In this study, we reconstruct phylogenetic relationships within Polygonatum and test its monophyly using a phylogenomic approach. For that, we built a comprehensive dataset that includes complete or nearly-complete plastid genomes of 19 species of Polygonatum, one of Disporopsis, and four of Heteropolygonatum. Their plastid genomes do not present any major structural differences and range from 153,821 to 155,580 bp in length. Molecular phylogenetic analyses of the chloroplast coding regions indicate that Polygonatum and Heteropolygonatum are monophyletic, providing support for their recognition as distinct genera and corroborating recent adjustments of their circumscriptions. An expanded analysis with higher species sampling using the petA-psbJ plastid gene region combined with the nuclear ribosomal ITS provided support for the recognition of three distinct sections within Polygonatum. These same sections are further supported by chromosome data: Polygonatum sect. Sibirica (x = 12); Polygonatum sect. Polygonatum (x = 9-11); and, Polygonatum sect. Verticillata (x = 13-15). Populations of P. multiflorum from northwestern Himalaya are here shown to be best treated as a separate taxon, P. govanianum. Furthermore, P. verticillatum is shown to be polyphyletic, indicating that it represents a species-complex that includes multiple Asiatic species. Despite that, additional studies are still needed until the proper nomenclatural adjustments can be made.

Keywords: Asparagales; Himalaya; Polygonateae; phylogeny

DOI: https://doi.org/10.1016/j.ympev.2018.08.017

Trends Plant Sci. 2018 Sep 05. pii: S1360-1385(18)30189-4. [Epub ahead of print]

The Rise of Cotton Genomics.

Syed Shan-E-Ali Zaidi, Shahid Mansoor, Andrew Paterson.

Cotton is the most important fiber crop, but its polyploid genome is complex and difficult to improve. Recent advances in obtaining high-quality genome sequences of cultivated tetraploid and diploid cotton species may now overcome this hurdle, as well as provide new insights on important fiber quality and disease resistance genes.

Keywords: Gossypium; cotton; fiber; plant breeding; plant genomics

DOI: https://doi.org/10.1016/j.tplants.2018.08.009

Virology. 2018 Sep 05. pii: S0042-6822(18)30257-5. [Epub ahead of print]524 127-139

Expression and antiviral function of ARGONAUTE 2 in Nicotiana benthamiana plants infected with two isolates of tomato ringspot virus with varying degrees of virulence.

Dinesh Babu Paudel, Basudev Ghoshal, Sushma Jossey, Marta Ludman, Karoly Fatyol, Hélène Sanfaçon.

ARGONAUTEs (notably AGO1 and AGO2) are effectors of plant antiviral RNA silencing. AGO1 was shown to be required for the temperature-dependent symptom recovery of Nicotiana benthamiana plants infected with tomato ringspot virus (isolate ToRSV-Rasp1) at 27 °C. In this study, we show that symptom recovery from isolate ToRSV-GYV shares similar hallmarks of antiviral RNA silencing but occurs at a wider range of temperatures (21-27 °C). At 21 °C, an early spike in AGO2 mRNAs accumulation was observed in plants infected with either ToRSV-Rasp1 or ToRSV-GYV but the AGO2 protein was only consistently detected in ToRSV-GYV infected plants. Symptom recovery from ToRSV-GYV at 21 °C was not prevented in an ago2 mutant or by silencing of AGO1 or AGO2. We conclude that other factors (possibly other AGOs) contribute to symptom recovery under these conditions. The results also highlight distinct expression patterns of AGO2 in response to ToRSV isolates and environmental conditions.

Keywords: Disease recovery; Nepovirus; Plant-virus interactions; RNA silencing; Symptom recovery

DOI: https://doi.org/10.1016/j.virol.2018.08.016