Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Zhou, Shan-Shan
Xing, Zhen
Liu, Hui
Hu, Xian-Ge
Gao, Qiong
Xu, Jie
Jiao, Si-Qian
Jia, Kai-Hua
Jin, Yu Q
Zhao, Wei
Porth, Ilga
El-Kassaby, Yousry A.
Mao, Jian-Feng

March 2019

Background: Cupressus gigantea, a rare and endangered tree species with remarkable ...

Additional file 6: of Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions

Norbert Bokros (6468503)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

Table S1. Table containing the Gossypium hirsutum transcriptome analysis results. The first sheet ha...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 5: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S2. Summary of database matches (specific values) for C. gigantea unigenes. (DOCX 15 kb

Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S3. Database matches (full results) for C. gigantea unigenes. (XLSX 1763 kb

Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S7. Functional enrichment analysis of the specific gene families from C. gigantea. The full li...

Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S8. Characteristics of the transcriptome assemblies from related conifer species and re-analys...

Additional file 16: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S9. Conserved motifs in LRR-RLK domain from C. gigantea transcriptome and their consensus seq...

Additional file 17: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S10. Alignment of the conserved RxR and DDxxD motifs and motifs variation among 121 TPS seque...

Additional file 12: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S6. Metabolic pathway of the Terpenoid bakcone biosynthesis for the unigenes identified in C....

Additional file 15: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S8. Multiple sequence alignment (MSA) of the USPA-like domains of the putative USPA protein. ...

Additional file 19: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S12. Test of differential gene expresssion among selected genes from three gene families (USP...

Additional file 18: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S11. Gel electrophoresis of 39 primers for real-time PCR with cDNA as template (a and b) and ...

Additional file 1: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S1. Assessment of reads by FastQC before quality control. a) Quality of raw-reads per base. T...

Additional file 2: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S2. Assessment of reads using FastQC after quality control. a) Quality of reads per base afte...

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Zhou, Shan-Shan
Xing, Zhen
Liu, Hui
Hu, Xian-Ge
Gao, Qiong
Xu, Jie
Jiao, Si-Qian
Jia, Kai-Hua
Jin, Yu Q
Zhao, Wei
Porth, Ilga
El-Kassaby, Yousry A.
Mao, Jian-Feng

March 2019

Background: Cupressus gigantea, a rare and endangered tree species with remarkable ...

Additional file 6: of Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions

Norbert Bokros (6468503)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

Table S1. Table containing the Gossypium hirsutum transcriptome analysis results. The first sheet ha...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 5: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S2. Summary of database matches (specific values) for C. gigantea unigenes. (DOCX 15 kb

Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S3. Database matches (full results) for C. gigantea unigenes. (XLSX 1763 kb

Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S7. Functional enrichment analysis of the specific gene families from C. gigantea. The full li...

Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Table S8. Characteristics of the transcriptome assemblies from related conifer species and re-analys...

Additional file 16: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S9. Conserved motifs in LRR-RLK domain from C. gigantea transcriptome and their consensus seq...

Additional file 17: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S10. Alignment of the conserved RxR and DDxxD motifs and motifs variation among 121 TPS seque...

Additional file 12: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S6. Metabolic pathway of the Terpenoid bakcone biosynthesis for the unigenes identified in C....

Additional file 15: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S8. Multiple sequence alignment (MSA) of the USPA-like domains of the putative USPA protein. ...

Additional file 19: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S12. Test of differential gene expresssion among selected genes from three gene families (USP...

Additional file 18: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S11. Gel electrophoresis of 39 primers for real-time PCR with cDNA as template (a and b) and ...

Additional file 1: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S1. Assessment of reads by FastQC before quality control. a) Quality of raw-reads per base. T...

Additional file 2: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Shan-Shan Zhou (4842522)
Zhen Xing (700481)
Hui Liu (33624)
Xian-Ge Hu (763677)
Qiong Gao (13880)
Jie Xu (34477)
Si-Qian Jiao (6456977)
Kai-Hua Jia (6456980)
Yu Jin (360487)
Wei Zhao (14321)
Ilga Porth (138357)
Yousry El-Kassaby (3298056)
Jian-Feng Mao (427222)

March 2019

Figure S2. Assessment of reads using FastQC after quality control. a) Quality of reads per base afte...

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

Zhou, Shan-Shan
Xing, Zhen
Liu, Hui
Hu, Xian-Ge
Gao, Qiong
Xu, Jie
Jiao, Si-Qian
Jia, Kai-Hua
Jin, Yu Q
Zhao, Wei
Porth, Ilga
El-Kassaby, Yousry A.
Mao, Jian-Feng

March 2019

Background: Cupressus gigantea, a rare and endangered tree species with remarkable ...

Additional file 6: of Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions

Norbert Bokros (6468503)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

Table S1. Table containing the Gossypium hirsutum transcriptome analysis results. The first sheet ha...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Abstract

Extracted data

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Abstract

Extracted data

Related items

Related items

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Abstract

Extracted data

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Abstract

Extracted data

Related items

Related items

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

Additional file 3: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues