Gene_locus Report for: poptr-a9pch4

Other strains: Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa); Populus alba (White poplar)

(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.)
> cellular organisms: N E > Eukaryota: N E > Viridiplantae: N E > Streptophyta: N E > Streptophytina: N E > Embryophyta: N E > Tracheophyta: N E > Euphyllophyta: N E > Spermatophyta: N E > Magnoliophyta: N E > Mesangiospermae: N E > eudicotyledons: N E > Gunneridae: N E > Pentapetalae: N E > rosids: N E > fabids: N E > Malpighiales: N E > Salicaceae: N E > Saliceae: N E > Populus: N E > Populus trichocarpa: N E

Title: De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
Liu YJ, Wang XR, Zeng QY
Ref: Sci China Life Sciences, 62:609, 2019 : PubMed
Abstract


ESTHER: Liu_2019_Sci.China.Life.Sci_62_609
PubMedSearch: Liu 2019 Sci.China.Life.Sci 62 609
PubMedID: 30661181
Gene_locus related to this paper: poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, popal-a0a4u5qy13, popal-a0a4u5mi39

Abstract

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170+/-0.014, which was lower than that in Italy (0.271+/-0.051) and Hungary (0.264+/-0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.



        

Title: Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding
Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA and Bohlmann J <2 more author(s)> Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJ, Marra MA, Bohlmann J (- 2)
Ref: BMC Genomics, 9:57, 2008 : PubMed
Abstract


ESTHER: Ralph_2008_BMC.Genomics_9_57
PubMedSearch: Ralph 2008 BMC.Genomics 9 57
PubMedID: 18230180
Gene_locus related to this paper: poptr-a9pbm5, poptr-a9pfp5, poptr-a9pgl0, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9gnp9, poptr-b9gyq1, poptr-b9hxr7, poptr-b9i9p8, poptr-a9pfa7, poptr-a9pch4, poptr-a9pfg4

Abstract

BACKGROUND: The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. RESULTS: As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa x P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars. CONCLUSION: This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838.



        

Title: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S and Rokhsar D <100 more author(s)> Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (- 100)
Ref: Science, 313:1596, 2006 : PubMed
Abstract


ESTHER: Tuskan_2006_Science_313_1596
PubMedSearch: Tuskan 2006 Science 313 1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31, delas-a9c1v9, poptr-a9pfp5, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9giq0, poptr-b9gjs0, poptr-b9gl72, poptr-b9gmx8, poptr-b9gnp9, poptr-b9gny4, poptr-b9grg2, poptr-b9gsc2, poptr-b9gvp3, poptr-b9gvs3, poptr-b9gwn9, poptr-b9gy32, poptr-b9gyq1, poptr-b9gys8, poptr-b9h0h0, poptr-b9h4j2, poptr-b9h6c2, poptr-b9h6c5, poptr-b9h6l8, poptr-b9h8c9, poptr-b9h301, poptr-b9h579, poptr-b9hbl2, poptr-b9hbw5, poptr-b9hcn9, poptr-b9hee0, poptr-b9hee2, poptr-b9hee5, poptr-b9hee6, poptr-b9hef3, poptr-b9hfa7, poptr-b9hfd3, poptr-b9hfi6, poptr-b9hft8, poptr-b9hg83, poptr-b9hif5, poptr-b9hll5, poptr-b9hmd0, poptr-b9hnv3, poptr-b9hqr6, poptr-b9hqr7, poptr-b9hrv7, poptr-b9hs66, poptr-b9huf0, poptr-b9hur3, poptr-b9hux1, poptr-b9hwp2, poptr-b9hxr7, poptr-b9hyk8, poptr-b9hyx2, poptr-b9i2q8, poptr-b9i5b8, poptr-b9i5j8, poptr-b9i5j9, poptr-b9i5k0, poptr-b9i6b6, poptr-b9i7b7, poptr-b9i9p8, poptr-b9i484, poptr-b9i994, poptr-b9ial3, poptr-b9ial4, poptr-b9ib28, poptr-b9ibr8, poptr-b9id97, poptr-b9idr4, poptr-b9iid9, poptr-b9iip0, poptr-b9ik80, poptr-b9ik90, poptr-b9il63, poptr-b9ink7, poptr-b9iqa0, poptr-b9iqd5, poptr-b9mwf1, poptr-b9mwi8, poptr-b9n0c6, poptr-b9n0n1, poptr-b9n0n4, poptr-b9n0z5, poptr-b9n1t8, poptr-b9n1z3, poptr-b9n3m7, poptr-b9n233, poptr-b9n236, poptr-b9n395, poptr-b9nd33, poptr-b9nd34, poptr-b9ndi6, poptr-b9ndj5, poptr-b9p9i8, poptr-a9pfa7, poptr-b9hdp2, poptr-b9inj0, poptr-b9n5g7, poptr-b9i8q4, poptr-u5g0r4, poptr-u5gf59, poptr-u7e1l9, poptr-b9hj61, poptr-b9hwd0, poptr-u5fz17, poptr-a0a2k2brq1, poptr-a0a2k2b9i6, poptr-a0a2k1x9y8, poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2a850, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, poptr-a0a2k2blg2, poptr-a0a2k1xpi3, poptr-a0a2k1xpj0, poptr-a0a2k2b331, poptr-a0a2k2byl7, poptr-b9iek5, poptr-a9pfg4, poptr-a0a2k1xzs5, poptr-b9gga9, poptr-b9guw6, poptr-b9hff2

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.